Analyse de la tâche d'un pilote de Rafale à l'aide d'une HTA étendue à la gestion des modes dégradés

International audienceCette communication présente l'adaptation de la méthode HTA pour l'étude d'une situation dynamique incertaine et coopérative : une mission militaire aérienne réalisée par un pilote de chasse à bord d'un avion Rafale. Les boucles - perception, représentation, action - caractéristiques de la gestion d'une situation dynamique sont intégrées dans la HTA sous la forme de buts de haut-niveau. La mise en évidence de plans contingents permet de rendre compte de la gestion de l'incertitude et des situations dégradées. Enfin, la coopération multiagents est décrite par un codage des tâches de communication précisant la fonction, l'objet et les acteurs impliqués. Finalement, les intérêts et les limites de l'application de la méthode HTA dans le cadre des situations dynamiques sont discutés

Proteomic and functional analyses of the virion transmembrane proteome of cyprinid herpesvirus 3

Virion transmembrane proteins (VTPs) mediate key functions in the herpesvirus infectious cycle. Cyprinid herpesvirus 3 (CyHV-3) is the archetype of fish alloherpesviruses. The present study was devoted to CyHV-3 VTPs. Using mass spectrometry approaches, we identified 16 VTPs of the CyHV-3 FL strain. Mutagenesis experiments demonstrated that eight of these proteins are essential for viral growth in vitro (ORF32, ORF59, ORF81, ORF83, ORF99, ORF106, ORF115, and ORF131), and eight are non-essential (ORF25, ORF64, ORF65, ORF108, ORF132, ORF136, ORF148, and ORF149). Among the non-essential proteins, deletion of ORF25, ORF132, ORF136, ORF148, or ORF149 affects viral replication in vitro, and deletion of ORF25, ORF64, ORF108, ORF132, or ORF149 impacts plaque size. Lack of ORF148 or ORF25 causes attenuation in vivo to a minor or major extent, respectively. The safety and efficacy of a virus lacking ORF25 were compared to those of a previously described vaccine candidate deleted for ORF56 and ORF57 (Δ56-57). Using quantitative PCR, we demonstrated that the ORF25 deleted virus infects fish through skin infection and then spreads to internal organs as reported previously for the wild-type parental virus and the Δ56-57 virus. However, compared to the parental wild-type virus, the replication of the ORF25 deleted virus was reduced in intensity and duration to levels similar to those observed for the Δ56-57 virus. Vaccination of fish with a virus lacking ORF25 was safe but had low efficacy at the doses tested. This characterization of the virion transmembrane proteome of CyHV-3 provides a firm basis for further research on alloherpesvirus VTPs. IMPORTANCE Virion transmembrane proteins play key roles in the biology of herpesviruses. Cyprinid herpesvirus 3 (CyHV-3) is the archetype of fish alloherpesviruses and the causative agent of major economic losses in common and koi carp worldwide. In this study of the virion transmembrane proteome of CyHV-3, the major findings were: (i) the FL strain encodes 16 virion transmembrane proteins; (ii) eight of these proteins are essential for viral growth in vitro; (iii) seven of the non-essential proteins affect viral growth in vitro, and two affect virulence in vivo; and (iv) a mutant lacking ORF25 is highly attenuated but induces moderate immune protection. This study represents a major breakthrough in understanding the biology of CyHV-3 and will contribute to the development of prophylactic methods. It also provides a firm basis for the further research on alloherpesvirus virion transmembrane proteins

Shotgun redox proteomics: identification and quantitation of carbonylated proteins in the UVB resistant marine bacterium, Photobacterium angustum S14

UVB oxidizes proteins through the generation of reactive oxygen species. One consequence of UVB irradiation is carbonylation, the irreversible formation of a carbonyl group on proline, lysine, arginine or threonine residues. In this study, redox proteomics was performed to identify carbonylated proteins in the UVB resistant marine bacterium Photobacterium angustum. Mass-spectrometry was performed with either biotin-labeled or dinitrophenylhydrazide (DNPH) derivatized proteins. The DNPH redox proteomics method enabled the identification of 62 carbonylated proteins (5% of 1221 identified proteins) in cells exposed to UVB or darkness. Eleven carbonylated proteins were quantified and the UVB/dark abundance ratio was determined at both the protein and peptide levels. As a result we determined which functional classes of proteins were carbonylated, which residues were preferentially modified, and what the implications of the carbonylation were for protein function. As the first large scale, shotgun redox proteomics analysis examining carbonylation to be performed on bacteria, our study provides a new level of understanding about the effects of UVB on cellular proteins, and provides a methodology for advancing studies in other biological systems

Exploration du potentiel bioindustriel des cultures pures ou mixtes de bactéries pourpres non sulfureuse en conditions photohétérotrophiques

Purple non-sulfur bacteria are well known for their metabolic versatility as they can grow under both auto-and heterotrophic conditions, phototrophically or not. Moreover, they are able to assimilate a broad range of carbon sources notably volatile fatty acids (VFAs, C1-C5) but also sugars. The PROTMIC lab (UMONS) developed a tremendous expertise in the understanding of metabolic pathways used by PNSB, and more precisely Rhodospirillum rubrum, to assimilate VFAs either pure (one source of carbon) or in mix (several source of carbon). This expertise allowed us to decipher the photoheterotrophic assimilation of different VFAs such as acetic acid, butyric acid or valeric acid. In that context, our lab investigated the production of polyhydroxyalkanoate by pure culture of Rhodospirillum rubrum cultivated under photoheterotrophic conditions using acetic acid or valeric acid as source of carbon. More precisely we studied the photoheterotrophic metabolism of Rs. rubrum in the here above-mentioned conditions in order to find some tracks for PHA production optimization. More recently, our lab started analysing the production of protein-rich purple bacteria biomass using bioindustrial co-products as source of carbon. We investigate, currently, at the fundamental (e.g. metabolic pathway, interaction,…) and applied (e.g. protein content, protein quality, productivity,…) point of view the assimilation of molasses by either pure or mix culture of purple bacteria and the impact of different consortia on productivity. Since more than ten years, PNSB are extensively studied for their bioindustrial applications (e.g. Pigment, PHAs, hydrogen, protein-rich edible biomass, wastewater treatment, …). However, in order for the different bioprocesses to be economically feasible, major optimization are still needed. In that context, two schools of thought are commonly found in the literature, the first one stating that the use of pure culture allows higher process optimization thanks to a better understanding whiled the second one arguing that the use of mix culture brings synergic effects that are a key parameter in process improvement. Here, we present examples of the application of these two different strategies to increase bioindustrial productivity of PNSB based bioprocesses. First, using pure culture of Rs. rubrum, we succeeded in increasing PHA production in the presence of acetic and valeric acid thanks to a fundamental knowledge-based approach (e.g. literature reviewing, proteomic analyses, growth under different conditions; Figures 1 and 2). Secondly, we observed recently an increased productivity and substrate assimilation efficiency by switching from pure (e.g. Rs rubrum) to mix (Rs.rubrum and Rh. capsulatus) culture (Figure 3)

Identification and localization of the structural proteins of anguillid herpesvirus 1

Many of the known fish herpesviruses have important aquaculture species as their natural host, and may cause serious disease and mortality. Anguillid herpesvirus 1 (AngHV-1) causes a hemorrhagic disease in European eel, Anguilla anguilla. Despite their importance, fundamental molecular knowledge on fish herpesviruses is still limited. In this study we describe the identification and localization of the structural proteins of AngHV-1. Purified virions were fractionated into a capsid-tegument and an envelope fraction, and premature capsids were isolated from infected cells. Proteins were extracted by different methods and identified by mass spectrometry. A total of 40 structural proteins were identified, of which 7 could be assigned to the capsid, 11 to the envelope, and 22 to the tegument. The identification and localization of these proteins allowed functional predictions. Our findings include the identification of the putative capsid triplex protein 1, the predominant tegument protein, and the major antigenic envelope proteins. Eighteen of the 40 AngHV-1 structural proteins had sequence homologues in related Cyprinid herpesvirus 3 (CyHV-3). Conservation of fish herpesvirus structural genes seemed to be high for the capsid proteins, limited for the tegument proteins, and low for the envelope proteins. The identification and localization of the structural proteins of AngHV-1 in this study adds to the fundamental knowledge of members of the Alloherpesviridae family, especially of the Cyprinivirus genus

Differential proteomics and physiology of Pseudomonas putida KT2440 under filament-inducing conditions

Abstract Background Pseudomonas putida exerts a filamentous phenotype in response to environmental stress conditions that are encountered during its natural life cycle. This study assessed whether P. putida filamentation could confer survival advantages. Filamentation of P. putida was induced through culturing at low shaking speed and was compared to culturing in high shaking speed conditions, after which whole proteomic analysis and stress exposure assays were performed. Results P. putida grown in filament-inducing conditions showed increased resistance to heat and saline stressors compared to non-filamented cultures. Proteomic analysis showed a significant metabolic change and a pronounced induction of the heat shock protein IbpA and recombinase RecA in filament-inducing conditions. Our data further indicated that the associated heat shock resistance, but not filamentation, was dependent of RecA. Conclusions This study provides insights into the altered metabolism of P. putida in filament-inducing conditions, and indicates that the formation of filaments could potentially be utilized by P. putida as a survival strategy in its hostile, recurrently changing habitat.</p

Skin mucus of Cyprinus carpio inhibits cyprinid herpesvirus 3 binding to epidermal cells

Cyprinid herpesvirus 3 (CyHV-3) is the aetiological agent of a mortal and highly contagious disease in common and koi carp. The skin is the major portal of entry of CyHV-3 in carp after immersion in water containing the virus. In the present study, we used in vivo bioluminescence imaging to investigate the effect of skin mucus removal and skin epidermis lesion on CyHV-3 entry. Physical treatments inducing removal of the mucus up to complete erosion of the epidermis were applied on a defined area of carp skin just before inoculation by immersion in infectious water. CyHV-3 entry in carp was drastically enhanced on the area of the skin where the mucus was removed with or without associated epidermal lesion. To investigate whether skin mucus inhibits CyHV-3 binding to epidermal cells, tail fins with an intact mucus layer or without mucus were inoculated ex vivo. While electron microscopy examination revealed numerous viral particles bound on the fins inoculated after mucus removal, no particle could be detected after infection of mucus-covered fins. Finally, anti-CyHV-3 neutralising activity of mucus extract was tested in vitro. Incubation of CyHV-3 with mucus extract reduced its infectivity in a dose dependent manner. The present study demonstrates that skin mucus removal and epidermal lesions enhance CyHV-3 entry in carp. It highlights the role of fish skin mucus as an innate immune protection against viral epidermal entry

A simple, verified validator for software pipelining

International audienceSoftware pipelining is a loop optimization that overlaps the execution of several iterations of a loop to expose more instruction-level parallelism. It can result in first-class performances characteristics, but at the cost of significant obfuscation of the code, making this optimization difficult to test and debug. In this paper, we present a translation validation algorithm that uses symbolic evaluation to detect semantics discrepancies between a loop and its pipelined version. Our algorithm can be implemented simply and efficiently, is provably sound, and appears to be complete with respect to most modulo scheduling algorithms. A conclusion of this case study is that it is possible and effective to use symbolic evaluation to reason about loop transformations