Caractérisation et régulation de la transcription antisens chez le VIH-1 et les rétrovirus HTLVs

On a longtemps cru que, chez les retrovirus, la production de la totalité des protéines virales dépendait de l'expression d'un transcrit sens de pleine longueur, initié dans le LTR 5'. Alors que la présence de transcription antisens chez les retrovirus a déjà été suggérée il y a plusieurs années, des preuves concrètes de son rôle biologique ont plus récemment été apportées grâce à une étude qui mettait en évidence l'identification d'une nouvelle protéine virale chez HTLV-1. En effet, cette protéine nommée HBZ est codée par un transcrit antisens épissé de façon alternative et initié dans le LTR 3'. De façon intéressante, la protéine HBZ est impliquée dans la régulation de la transcription virale et est capable d'inhiber la transcription dépendante du transactivateur viral Tax. Ces nouvelles données laissaient donc croire que la transcription antisens pourrait également exister chez d'autres retrovirus, compte tenu de la présence d'un ORF conservé dans le brin positif de l'ADN proviral de plusieurs d'entre eux. Les principaux objectifs de ce projet étaient d'étudier la régulation du transcrit antisens chez HTLV-1 et d'évaluer la présence de transcription antisens chez le VIH-1 ainsi que chez les retrovirus humains HTLV-3 et HTLV-4. Premièrement, les résultats obtenus démontrent que la protéine virale Tax est un facteur important dans le contrôle de la transcription antisens chez HTLV-1 et que son action est dépendante de CREB. De plus, nos résultats suggèrent fortement que les sites d'intégration dans le génome de la cellule hôte ont un impact important sur le niveau d'expression du transcrit antisens en absence ou en présence de Tax. De façon intéressante, des analyses de RT-PCR ont permis de démontrer la présence de transcrits antisens épissés dans les cellules transfectées par des clones moléculaires complets d'HTLV-3 et HTLV-4. Des analyses additionnelles ont pu mettre en évidence la localisation majoritairement nucléaire des protéines codées par ces transcrits. Nos résultats démontrent que ces protéines, nommées APH-3 et APH-4, ont également la capacité d'inhiber l'action de Tax. Dans un second temps, l'utilisation d'un protocole de RT-PCR brin-spécifique a permis la détection de transcrits antisens dans plusieurs lignées cellulaires infectées par le VIH-1. La présence de transcription antisens au cours du cycle de replication viral a pu être clairement établie par l'utilisation d'un virus pseudotypé contenant le gène rapporteur luciférase positionné en orientation antisens. La protéine antisens du VIH-1 (ASP) a ensuite été exprimée et détectée efficacement dans les cellules d'insectes SF9 ainsi que dans les cellules de mammifères COS-7 et 293T. Ces nouvelles données indiquent que la transcription antisens est une stratégie répandue chez les retrovirus et suggèrent qu'une analyse approfondie du phénomène est nécessaire à une meilleure compréhension du cycle de replication retroviral

Non-deforestation fire vs. fossil fuel combustion: the source of CO₂ emissions affects the global carbon cycle and climate responses

Non-deforestation fire – i.e., fire that is typically followed by the recovery of natural vegetation – is arguably the most influential disturbance in terrestrial ecosystems, thereby playing a major role in carbon exchanges and affecting many climatic processes. The radiative effect from a given atmospheric CO2 perturbation is the same for fire and fossil fuel combustion. However, major differences exist per unit of CO2 emitted between the effects of non-deforestation fire vs. fossil fuel combustion on the global carbon cycle and climate, because (1) fossil fuel combustion implies a net transfer of carbon from geological reservoirs to the atmospheric, oceanic, and terrestrial pools, whereas fire occurring in terrestrial ecosystems does not; (2) the average lifetime of the atmospheric CO2 increase is longer when originating from fossil fuel combustion compared to fire, due to the strong vegetation regrowth following fire disturbances in terrestrial ecosystems; and (3) other impacts, for example on land surface albedo, also differ between fire and fossil fuel combustion. The main purpose of this study is to illustrate the consequences from these fundamental differences between fossil fuel combustion and non-deforestation fires using 1000-year simulations of a coupled climate–carbon model with interactive vegetation. We assessed emissions from both pulse and stable fire regime changes, considering both the gross (carbon released from combustion) and net (fire-caused change in land carbon, also accounting for vegetation decomposition and regrowth, as well as climate–carbon feedbacks) fire CO2 emissions. In all cases, we found substantial differences from equivalent amounts of emissions produced by fossil fuel combustion. These findings suggest that side-by-side comparisons of non-deforestation fire and fossil fuel CO2 emissions – implicitly implying that they have similar effects per unit of CO2 emitted – should therefore be avoided, particularly when these comparisons involve gross fire emissions, because the reservoirs from which these emissions are drawn have very different residence times (millions of years for fossil fuel; years to centuries for vegetation and soil–litter). Our results also support the notion that most net emissions occur relatively soon after fire regime shifts and then progressively approach zero. Overall, our study calls for the explicit representation of fire activity as a valuable step to foster a more accurate understanding of its impacts on global carbon cycling and temperature, as opposed to conceiving fire effects as congruent with the consequences from fossil fuel combustion

Non-deforestation fire vs. fossil fuel combustion: the source of CO2 emissions affects the global carbon cycle and climate responses

Non-deforestation fire – i.e., fire that is typically followed by the recovery of natural vegetation – is arguably the most influential disturbance in terrestrial ecosystems, thereby playing a major role in carbon exchanges and affecting many climatic processes. The radiative effect from a given atmospheric CO2 perturbation is the same for fire and fossil fuel combustion. However, major differences exist per unit of CO2 emitted between the effects of non-deforestation fire vs. fossil fuel combustion on the global carbon cycle and climate, because (1) fossil fuel combustion implies a net transfer of carbon from geological reservoirs to the atmospheric, oceanic, and terrestrial pools, whereas fire occurring in terrestrial ecosystems does not; (2) the average lifetime of the atmospheric CO2 increase is longer when originating from fossil fuel combustion compared to fire, due to the strong vegetation regrowth following fire disturbances in terrestrial ecosystems; and (3) other impacts, for example on land surface albedo, also differ between fire and fossil fuel combustion. The main purpose of this study is to illustrate the consequences from these fundamental differences between fossil fuel combustion and non-deforestation fires using 1000-year simulations of a coupled climate–carbon model with interactive vegetation. We assessed emissions from both pulse and stable fire regime changes, considering both the gross (carbon released from combustion) and net (fire-caused change in land carbon, also accounting for vegetation decomposition and regrowth, as well as climate–carbon feedbacks) fire CO2 emissions. In all cases, we found substantial differences from equivalent amounts of emissions produced by fossil fuel combustion. These findings suggest that side-by-side comparisons of non-deforestation fire and fossil fuel CO2 emissions – implicitly implying that they have similar effects per unit of CO2 emitted – should therefore be avoided, particularly when these comparisons involve gross fire emissions, because the reservoirs from which these emissions are drawn have very different residence times (millions of years for fossil fuel; years to centuries for vegetation and soil–litter). Our results also support the notion that most net emissions occur relatively soon after fire regime shifts and then progressively approach zero. Overall, our study calls for the explicit representation of fire activity as a valuable step to foster a more accurate understanding of its impacts on global carbon cycling and temperature, as opposed to conceiving fire effects as congruent with the consequences from fossil fuel combustion

Detection, characterization and regulation of antisense transcripts in HIV-1

© 2007 Landry et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution Licens

Determination of Hydroacoustic Draft Tube Parameters by High Speed Visualization during Model Testing of a Francis Turbine

Francis turbines can experience critical instabilities at high load operating points, limiting their maximum power output. The swirling flow developed in the draft tube produces a cavitating axisymmetric volume, acting as an internal energy source leading to a self-excited surge phenomenon. The pulsation of the vortex rope corresponds to one of the eigenfrequencies of the hydraulic system. Efforts to accurately characterize, simulate and predict this phenomenon have been undertaken by several researchers, using a 1-D hydroacoustic model of the full load vortex rope. The key physical parameters are the mass flow gain factor, standing for the excitation mass source of the hydraulic system, the cavitation compliance factor, representing the wave speed and the thermodynamic damping, modeling the energy dissipation between the liquid and the gas. These parameters need to be determined either numerically or experimentally. The aim of the present investigation is to determine the mass flow gain factor and the cavitation compliance using experimental data obtained during a measurement campaign on a reduced scale Francis turbine model and to compare the results to existing CFD data

Non-Linear Stability Analysis of a Reduced Scale Model Pump-Turbine at Off-Design Operation

Nowadays, the pump-storage power plants are a proven solution for storing electricity at large scale and offering flexibility to the power management. Therefore, the hydraulic machines are increasingly subject to off-design operation, start-up and shutdown sequences. However, the fast and frequent switching between pumping mode and generating mode presents technical challenges. In the present study, the reduced scale model of a low specific speed pump-turbine is investigated in generating mode at off-design conditions. The operation in the typical “S-shaped” curve of pump-turbine may become unstable and the machine may switch back and forth from generating mode to reverse pumping mode preventing the correct experimental survey of this part during the model testing. The instability has been solved by a testing procedure imposing a restriction of section and a control valve for being able to increase the energy losses. This procedure, commonly used in model testing of pump-turbines, significantly improves the stability of the machine and allows for the survey of the entire “S-curve”. The aim of the present investigation is to understand and explain the origin of the switch to reverse pumping mode. Thus, a hydro-acoustic test rig model was developed with the In-house EPFL SIMSEN software and a comparison between the systems with and without a restriction of section was studied. A numerical analysis indicates that the operating points of a pump-turbine system are defined by the solution of the equation relating the test rig characteristic and the energy-discharge characteristic of the hydraulic machine for a given rotational speed and a constant guide vanes opening. Furthermore, the addition of a restriction alters the curvature of the test rig characteristic and creates a new degree of freedom to achieve stable operating points in the “S-curve”. Finally, to ensure the stability of each operating points described by the numerical model, an eigenvalue study of the non-linear hydraulic system is necessary

Reduced scale model testing for prediction of eigenfrequencies and hydro-acoustic resonances in hydropower plants operating in off-design conditions

The massive penetration of the electrical network by renewable energy sources, such as wind and solar, pushes the operators to extend hydropower plant units operating range to meet the transmission system operator requirements. However, in off-design operating conditions, flow instabilities are developing in Francis turbines, inducing cavitation, pressure pulsations and potentially resonance that can threaten the stability of the whole system. Reduced scale model testing is commonly performed to assess the hydraulic behaviour of the machine for industrial projects. However, it is not possible to directly transpose pressure pulsations and resonance conditions from model to prototype since the characteristics of the hydraulic circuits are different from model to prototype. In this paper, a methodology developed in the framework of the HYPERBOLE European research project for predicting the eigenfrequencies of hydropower plant units operating in off-design conditions is introduced. It is based on reduced scale model testing and proper one-dimensional modelling of the hydraulic circuits, including the draft tube cavitation flow, at both the model and prototype scales. The hydro-acoustic parameters in the draft tube are identified at the model scale for a wide number of operating conditions and, then, transposed to the full-scale machine, together with the precession frequency for part load conditions. This enables the prediction of the eigenfrequencies and resonance conditions of the full-scale generating unit

HTLV-I antisense transcripts initiating in the 3'LTR are alternatively spliced and polyadenylated

BACKGROUND: Antisense transcription in retroviruses has been suggested for both HIV-1 and HTLV-I, although the existence and coding potential of these transcripts remain controversial. Thorough characterization is required to demonstrate the existence of these transcripts and gain insight into their role in retrovirus biology. RESULTS: This report provides the first complete characterization of an antisense retroviral transcript that encodes the previously described HTLV-I HBZ protein. In this study, we show that HBZ-encoding transcripts initiate in the 3' long terminal repeat (LTR) at several positions and consist of two alternatively spliced variants (SP1 and SP2). Expression of the most abundant HBZ spliced variant (SP1) could be detected in different HTLV-I-infected cell lines and importantly in cellular clones isolated from HTLV-I-infected patients. Polyadenylation of HBZ RNA occurred at a distance of 1450 nucleotides downstream of the HBZ stop codon in close proximity of a typical polyA signal. We have also determined that translation mostly initiates from the first exon located in the 3' LTR and that the HBZ isoform produced from the SP1 spliced variant demonstrated inhibition of Tax and c-Jun-dependent transcriptional activation. CONCLUSION: These results conclusively demonstrate the existence of antisense transcription in retroviruses, which likely plays a role in HTLV-I-associated pathogenesis through HBZ protein synthesis

A mechanism for the suppression of homologous recombination in G1 cells

DNA repair by homologous recombination (HR)(1) is highly suppressed in G1 cells(2,3) to ensure that mitotic recombination occurs solely between sister chromatids(4). Although many HR factors are cell cycle-regulated, the identity of the events that are both necessary and sufficient to suppress recombination in G1 cells is unknown. Here we report that the cell cycle controls the interaction of BRCA1 with PALB2-BRCA2 in order to constrain BRCA2 function to the S/G2 phases. We found that the BRCA1-interaction site on PALB2 is targeted by an E3 ubiquitin ligase composed of KEAP1, a PALB2-interacting protein(5), in complex with CUL3-RBX1(6). PALB2 ubiquitylation suppresses its interaction with BRCA1 and is counteracted by the deubiquitylase USP11, which is itself under cell cycle control. Restoration of the BRCA1-PALB2 interaction combined with the activation of DNA end resection is sufficient to induce HR in G1, as measured by RAD51 recruitment, unscheduled DNA synthesis and a CRISPR/Cas9-based gene targeting assay. We conclude that the mechanism prohibiting HR in G1 minimally consists of the suppression of DNA end resection coupled to a multi-step block to BRCA2 recruitment to DNA damage sites that involves the inhibition of BRCA1-PALB2-BRCA2 complex assembly. We speculate that the ability to induce HR in G1 cells with defined factors could spur the development of gene targeting applications in non-dividing cells