Mutations in matrix and SP1 repair the packaging specificity of a Human Immunodeficiency Virus Type 1 mutant by reducing the association of Gag with spliced viral RNA

<p>Abstract</p> <p>Background</p> <p>The viral genome of HIV-1 contains several secondary structures that are important for regulating viral replication. The stem-loop 1 (SL1) sequence in the 5' untranslated region directs HIV-1 genomic RNA dimerization and packaging into the virion. Without SL1, HIV-1 cannot replicate in human T cell lines. The replication restriction phenotype in the SL1 deletion mutant appears to be multifactorial, with defects in viral RNA dimerization and packaging in producer cells as well as in reverse transcription of the viral RNA in infected cells. In this study, we sought to characterize SL1 mutant replication restrictions and provide insights into the underlying mechanisms of compensation in revertants.</p> <p>Results</p> <p>HIV-1 lacking SL1 (NLΔSL1) did not replicate in PM-1 cells until two independent non-synonymous mutations emerged: G913A in the matrix domain (E42K) on day 18 postinfection and C1907T in the SP1 domain (P10L) on day 11 postinfection. NLΔSL1 revertants carrying either compensatory mutation showed enhanced infectivity in PM-1 cells. The SL1 revertants produced significantly more infectious particles per nanogram of p24 than did NLΔSL1. The SL1 deletion mutant packaged less HIV-1 genomic RNA and more cellular RNA, particularly signal recognition particle RNA, in the virion than the wild-type. NLΔSL1 also packaged 3- to 4-fold more spliced HIV mRNA into the virion, potentially interfering with infectious virus production. In contrast, both revertants encapsidated 2.5- to 5-fold less of these HIV-1 mRNA species. Quantitative RT-PCR analysis of RNA cross-linked with Gag in formaldehyde-fixed cells demonstrated that the compensatory mutations reduced the association between Gag and spliced HIV-1 RNA, thereby effectively preventing these RNAs from being packaged into the virion. The reduction of spliced viral RNA in the virion may have a major role in facilitating infectious virus production, thus restoring the infectivity of NLΔSL1.</p> <p>Conclusions</p> <p>HIV-1 evolved to overcome a deletion in SL1 and restored infectivity by acquiring compensatory mutations in the N-terminal matrix or SP1 domain of Gag. These data shed light on the functions of the N-terminal matrix and SP1 domains and suggest that both regions may have a role in Gag interactions with spliced viral RNA.</p

Models and modelling processes: A critical step for an environmental research [La modélisation: Moment critique des recherches sur l'environnement]

International audienceMany new modelling practices appeared over the last 20 years. These innovations together with the idiosyncrasies of environmental management issues stimulate social sciences to renew their approach and adapt their analysis of models and modelling processes. In particular, the new modelling practices have to be analysed in a historical and sociological perspective in order to better understand the role of modellers and user communities, as well as their interactions. This shift in focus, from models as objects to modelling processes as sets of practices, enables to reinstate the role of the different actors of modelling processes. Such an evolution of perspective is all the more necessary since environmental models are developed in an ever-closer relationship with action. Dealing with modellers aiming - through their tools - to "change the world", social scientists have to take into account the models' implementation and the context of use. This opens the way for a proper understanding of both their nature and their role in environmental management. These observations provide the very basis of a research domain that has been explored far less by social scientist in France than in Anglo-Saxons countries. A large research project entitled "Modelling, Simulations and Complex Systems Management" and funded by the French Ministry of Research is trying to fill this gap. The project aims at: (a) exchanging experiences between many disciplines, as diverse as History of Sciences, Epistemology, Management Sciences, Communication Sciences, Environmental Economics, Urban Transportation Economics, Climate Modelling or Chemistry ; (b) developing common concepts and understanding of these new environmental modelling approaches, (c) improve our understanding and characterisation of complex models, and, (d) renew our understanding of the role and status of models in environmental management. © 2003 Éditions scientifiques et médicales Elsevier SAS. Tous droits réservés

Long term prospective of the Seine River system: Confronting climatic and direct anthropogenic changes

International audienceTo explore the evolution of a human impacted river, the Seine (France), over the 21st century, three driving factors were examined: climate, agriculture, and point source inputs of domestic and industrial origin. Three future scenarios were constructed, by modification of a baseline representative of recent conditions. A climate change scenario, based on simulations by a general circulation model driven by the SRES-A2 scenario of radiative forcing, accounts for an average warming of + 3.3 °C over the watershed and marked winter increase and summer decrease in precipitation. To illustrate a possible reduction in nitrate pollution from agricultural origin, a scenario of good agricultural practices was considered, introducing catch crops and a 20% decrease in nitrogen fertilisation. Future point source pollution was estimated following the assumptions embedded in scenario SRES-A2 regarding demographic, economic and technologic changes, leading to reductions of 30 to 75% compared to 2000, depending on the pollutants. Four models, addressing separate components of the river system (agronomical model, hydrogeological model, land surface model and water quality model), were used to analyse the relative impact of these scenarios on water quality, in light of their impact on hydrology and crop production. The first-order driving factor of water quality over the 21st century is the projected reduction of point source pollution, inducing a noticeable decrease in eutrophication and oxygen deficits downstream from Paris. The impact of climate change on these terms is driven by the warming of the water column. It enhances algal growth in spring and the loss factors responsible for phytoplankton mortality in late summer (grazers and viruses). In contrast, increased seasonal contrasts in river discharge have a negligible impact on river water quality, as do the changes in riverine nitrate concentration, which never gets limiting. The latter changes have a similar magnitude under the three scenarios. Under climate change, riverine and groundwater nitrate concentrations increase and crop production is advantaged with reduced growing cycles and increased yields. In contrast, nitrate concentrations decrease under the good agricultural practices scenario, with a limited decrease in crop production. When these two scenarios are combined, the changes in nitrate concentrations balance each other and crop yields increase. The results of this numerical exercise indicate that the potential changes to the Seine River system during the 21st century will not lead to severely degraded water quality