Journal of Next-Generation Research 5.0
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Collaborative Processes Management: from Modeling to Enacting
No full textNational audienceCollaborative work is a complex activity that involves several actors thus managing it is complicated. This article addresses some matters of controlling collaborative work in the point of view of process management. The underlying objective is to discuss the issues from modeling to enacting collaborative processes in existing process management systems. To overcome the discussed problems, we are developing a process management framework that integrates directly the concept of collaborative task into both modeling language and enacting mechanism. Moreover, we propose a flexible approach that enables users to choose dynamically a suitable way to enact their collaborative tasks
SIVcol Nef counteracts SERINC5 by promoting its proteasomal degradation but does not efficiently enhance HIV-1 replication in human CD4+ T cells and lymphoid tissue
No full textInternational audienceSERINC5 is a host restriction factor that impairs infectivity of HIV-1 and other primate lentiviruses and is counteracted by the viral accessory protein Nef. However, the importance of SERINC5 antagonism for viral replication and cytopathicity remained unclear. Here, we show that the Nef protein of the highly divergent SIVcol lineage infecting mantled guerezas (Colobus guereza) is a potent antagonist of SERINC5, although it lacks the CD4, CD3 and CD28 down-modulation activities exerted by other primate lentiviral Nefs. In addition, SIVcol Nefs decrease CXCR4 cell surface expression, suppress TCR-induced actin remodeling, and counteract Colobus but not human tetherin. Unlike HIV-1 Nef proteins, SIVcol Nef induces efficient proteasomal degradation of SERINC5 and counteracts orthologs from highly divergent vertebrate species, such as Xenopus frogs and zebrafish. A single Y86F mutation disrupts SERINC5 and tetherin antagonism but not CXCR4 down-modulation by SIVcol Nef, while mutation of a C-proximal di-leucine motif has the opposite effect. Unexpectedly, the Y86F change in SIVcol Nef had little if any effect on viral replication and CD4+ T cell depletion in preactivated human CD4+ T cells and in ex vivo infected lymphoid tissue. However, SIVcol Nef increased virion infectivity up to 10-fold and moderately increased viral replication in resting peripheral blood mononuclear cells (PBMCs) that were first infected with HIV-1 and activated three or six days later. In conclusion, SIVcol Nef lacks several activities that are conserved in other primate lentiviruses and utilizes a distinct proteasome-dependent mechanism to counteract SERINC5. Our finding that evolutionarily distinct SIVcol Nefs show potent anti-SERINC5 activity supports a relevant role of SERINC5 antagonism for viral fitness in vivo. Our results further suggest this Nef function is particularly important for virion infectivity under conditions of limited CD4+ T cell activation
Understanding Fluid Flow during Tectonic Reactivation: An Example from the Flamborough Head Chalk Outcrop (UK)
No full textInternational audienceFlamborough Head chalks are located at the extremities of E-W and N-S trending fault systems along the Yorkshire coast (UK). Rock deformation is expressed in Selwicks Bay where a normal fault is exposed along with a high density of calcite veins. The fault mineralization is tested using geochemistry. Crosscutting relationships are used to differentiate between three vein generations: a network of parallel veins that are oriented perpendicular to stratigraphy (Group I), hydraulic breccia with typical jigsaw puzzle structure (Group II), and a third generation of calcite veins crosscutting the two previous generations (Group III). Geochemical analyses revealed that all three generations possess the same chemical signature and must reflect successive pulses from the same mineralizing fluid source. Strontium isotope analyses showed that the veins have elevated 87 Sr/ 86 Sr ratios, that is, up to 7.110, while ratios of the chalk matrix equal 7.707. The latter value is in agreement with the signature of Late Cretaceous seawater. Consequently, the source of the fluid is external, reflecting an open system. The radiogenic Sr-isotope ratios, combined with low iron concentration, suggest that fluids migrated through sandy deposits. Fluid inclusion salinities range from 0 to 12 eq. wt% NaCl equiv. with a dominance of very low salinity inclusions, reflecting a meteoric signal. This leads to a model where meteoric fluids stored in an underlying confined sandstone aquifer were remobilized. The wide range of salinities could result from mixing of the meteoric fluid with some more saline fluids present in the rock sequence or from the dissolution of salts in the subsurface. In addition to the understanding of the local paragenetic evolution of the veining in Flamborough Head chalks, this study offers an insight into the way how fluid flows and mineralizes along fault zones
: Practicing interdisciplinarity: a review of the Second Austral Summer School on vulnerability of coral reefs heritage (EEA VulPaRe 2016)
No full textInternational audienceIn November 2016, the Second Austral Summer School “Vulnerability of coral reefs heritage” (EEA VulPaRe 2016) took place at Toliara (Madagascar). The school was funded and organised by IRD (French Research Institute for Development) and IHSM (Institute of Halieutics and Marine Science, University of Toliara), and proposed an interdisciplinary approach to the study of coral reefs. Environmental issues, different types of knowledge and valorisation of coral reefs were addressed by means of lectures, seminars, discussions and fieldwork. In this paper, the participants of EEA VulPaRe 2016 provide a critical feedback on this original interdisciplinary research training.En novembre 2016, s’est tenue à Toliara, dans le sud-ouest de Madagascar, la deuxième école d’été australe sur la vulnérabilité du patrimoine récifal (EEA VulPaRe). Coorganisée par l’IRD (Institut de recherche pour le développement, France) et l’IHSM (Institut halieutique et des sciences marines de l’Université de Toliara, Madagascar), cette formation a proposé une approche interdisciplinaire de la thématique des récifs coralliens. Elle a été dispensée sous la forme de cours magistraux, de pratiques de terrain et de débats portant sur les questions environnementales, de connaissance, de valorisation et de conservation de ces milieux. Les participants de l’EEA VulPaRe 2016 souhaitent, à travers le présent article, donner à la communauté scientifique un retour d’expérience critique sur une démarche originale de formation à la recherche interdisciplinaire
Mineralizations and transition metal mobility driven by organic carbon during low-temperature serpentinization
No full textInternational audienceSerpentinization is known to provide substantial amounts of energy in the form of molecular hydrogen along with a suite of abiotic organic compounds of low molecular weight (mainly as short chain alkanes and carboxylic acids), all sustaining the development of microbial ecosystems in the mantle-derived crust. The latter have a cryptoendolithic life style and are responsible for (i) the local formation of biomass and of organic metabolic byproducts and (ii) the production of extracellular polymeric substances which organize the community in the form of a biofilm at the surface of the rock-forming minerals. In accordance, whatever their origin, organic compounds can be diverse and widespread in the shallow oceanic crust where they undergo hydrothermal degradation and remobilization through fluid circulations. Here we show that organic carbon is directly involved in low temperature serpentinization reactions (< 200 °C). Fine scale investigations of microbial niches hosted in serpentinites from the Mid-Atlantic ridge were performed using scanning and transmission electron microscopy along with scanning transmission X-ray microscopy. They suggest that organic coatings at mineral surfaces may influence the nature and structure of the serpentinization products as well as the mobility and speciation of transition metals as the reaction progresses. This likely constitutes an efficient yet poorly considered mechanism in active serpentinizing systems with possible implications for ore formation associated with the alteration of ophiolitic massifs and subsurface storage
Comparison of different nucleic acid preparation methods to improve specific HIV-1 RNA isolation for viral load testing on dried blood spots
No full textInternational audienceIn resource-limited countries (RLCs), WHO recommends HIV viral load (VL) on dried blood spots (DBS) for antiretroviral therapy (ART) monitoring of patients living in non-urban settings where plasma VL is not available. In order to reduce the impact of proviral DNA interference, leading to false positive results in samples with low plasma VL, we compared three different nucleic acid preparation methods with the NucliSens (Biomérieux) extraction, known for its high recovery of nucleic acids on DBS. Paired plasma-DBS samples (n = 151) with predominantly low plasma VL (≤ 10,000 copies/ml; 74%) were used. At the threshold of 1,000 copies/ml on DBS, 51% and 10% were misclassified as false positives or false negatives, respectively with NucliSens, versus 41% and 20% with m2000sp (Abbott), described as more specific for RNA recovery. DNase treatments of nucleic acid extracts and free virus elution (FVE) protocol before nucleic acid extraction, reduced the proportion of false positives to 0% and 19%, but increased the proportion of false negatives to 40% and 73%. More efforts are thus still needed to improve performance of VL assays on DBS to monitor patients on ART in RLCs and allow timely switch to more costly second or third line ART regimes
Using the OpenStreetMap database to improve an object-based classification process. Application to a landcover product on small islands in the Indian Ocean
No full textInternational audienceThe southwest of the Indian Ocean comprises numerous islands of less than 3000 sq km (Comoros, Seychelles, Mascarene Islands). These small island territories have very fragmented and diversified environments. Satellite imagery and products at low and medium spatial resolution (usually from 4 kilometers to 250 meters) are not or poorly suited to the study of these areas. This is particularly the case for ecological studies such as the study of vector-borne diseases where the evaluation of interactions at a fine scale is critical to understand their spatial dynamics. To overcome this need, we realized a homogeneous land cover mapping of these small islands, by analysing SPOT 5 satellite images acquired between July 2013 and July 2014 by SEAS-OI Station. We used an object-based image analysis method to identify the 12 major classes of land cover / land use of these tropical islands. To improve the results of this classification, we used some data from the free and participative OpenStreetMap (OSM) database as training data. These data were first checked and even completed to ensure their quality. This information helped us in particular to improve our results on agricultural areas (sugar cane, market gardening) and to define more precisely the main roads. This methodology together with a good knowledge of the field has enabled us to achieve an overall accuracy of 85%, making it an operational product. In return, we fed the OSM database by integrating the classes for which we had the best accuracy (mangrove, surface water and forest). Indeed, OSM is a particularly interesting platform for releasing and disseminating land use data