Caractérisation des mécanismes de réplication et de pathogenèse du viroïde de la mosaïque latente du pêcher (PLMVd)

Les viroïdes sont de petits ARN circulaires simple brin qui infectent les plantes supérieures, causant ainsi d'importantes pertes économiques dans le domaine agroalimentaire. Ces ARN ne sont pas encapsidés et se répliquent par un mécanisme en cercle roulant. Puisqu'ils ne semblent coder pour aucune protéine, les viroïdes sont dépendants de la machinerie enzymatique de l'hôte pour les différentes étapes de leur cycle de vie. La trentaine d'espèces différentes de viroïdes connues à ce jour sont classées en 2 grandes familles, celle des Pospiviroidae et celle des Avsunviroidae. Ces derniers sont caractérisés par la présence de séquences permettant l'adoption de la structure autocatalytique en tête de marteau (hammerhead) qui est responsable de la coupure des brins multimériques en monomères dans le cycle de réplication de ces viroïdes. Le but de mon projet de recherches était de mieux comprendre les différents mécanismes régissant les différentes étapes du cycle de vie des membres de la famille des Avsunviroidae, plus précisément du viroïde responsable de la mosaïque latente du pêcher (PLMVd). Dans un premier temps, nous avons démontré que PLMVd peut être recircularisé in vitro par un mécanisme d'autoligation. Il s'agit d'une démonstration originale d'une telle réaction en biologie et plusieurs aspects de cette réaction non-enzymatique ont été mis à jour. Dans un second temps, des expériences d'initiation de la réplication utilisant l'ARN polymérase de E. coli, qui est fortement similaire à la polymérase de type bactérienne du chloroplaste, ont démontré que celle-ci pouvait répliquer des transcrits de PLMVd in vitro . Dans un autre ordre d'idée, la possibilité que la pathogenèse de PLMVd puisse être le résultat d'une coupure en trans d'un ARN de l'hôte par la structure hammerhead de celui-ci a été étudiée. Finalement, des études structurales ont permis de déterminer la structure secondaire de PLMVd en solution. Celle-ci révèle la présence de plusieurs éléments conservés chez certains membres de la famille des Avsunviroidae. Ces résultats sont un premier pas vers la compréhension des relations structure/fonction chez ces ARN. De manière générale, ces recherches ont permis de mettre à jour plusieurs nouvelles fonctions associées aux séquences hammerhead."--Résumé abrégé par UM

ABINIT: Overview and focus on selected capabilities

Paper published as part of the special topic on Electronic Structure SoftwareABINIT is probably the first electronic-structure package to have been released under an open-source license about 20 years ago. It implements density functional theory, density-functional perturbation theory (DFPT), many-body perturbation theory (GW approximation and Bethe–Salpeter equation), and more specific or advanced formalisms, such as dynamical mean-field theory (DMFT) and the “temperaturedependent effective potential” approach for anharmonic effects. Relying on planewaves for the representation of wavefunctions, density, and other space-dependent quantities, with pseudopotentials or projector-augmented waves (PAWs), it is well suited for the study of periodic materials, although nanostructures and molecules can be treated with the supercell technique. The present article starts with a brief description of the project, a summary of the theories upon which ABINIT relies, and a list of the associated capabilities. It then focuses on selected capabilities that might not be present in the majority of electronic structure packages either among planewave codes or, in general, treatment of strongly correlated materials using DMFT; materials under finite electric fields; properties at nuclei (electric field gradient, Mössbauer shifts, and orbital magnetization); positron annihilation; Raman intensities and electro-optic effect; and DFPT calculations of response to strain perturbation (elastic constants and piezoelectricity), spatial dispersion (flexoelectricity), electronic mobility, temperature dependence of the gap, and spin-magnetic-field perturbation. The ABINIT DFPT implementation is very general, including systems with van der Waals interaction or with noncollinear magnetism. Community projects are also described: generation of pseudopotential and PAW datasets, high-throughput calculations (databases of phonon band structure, second-harmonic generation, and GW computations of bandgaps), and the library LIBPAW. ABINIT has strong links with many other software projects that are briefly mentioned.This work (A.H.R.) was supported by the DMREF-NSF Grant No. 1434897, National Science Foundation OAC-1740111, and U.S. Department of Energy DE-SC0016176 and DE-SC0019491 projects. N.A.P. and M.J.V. gratefully acknowledge funding from the Belgian Fonds National de la Recherche Scientifique (FNRS) under Grant No. PDR T.1077.15-1/7. M.J.V. also acknowledges a sabbatical “OUT” grant at ICN2 Barcelona as well as ULiège and the Communauté Française de Belgique (Grant No. ARC AIMED G.A. 15/19-09). X.G. and M.J.V. acknowledge funding from the FNRS under Grant No. T.0103.19-ALPS. X.G. and G.-M. R. acknowledge support from the Communauté française de Belgique through the SURFASCOPE Project (No. ARC 19/24-057). X.G. acknowledges the hospitality of the CEA DAM-DIF during the year 2017. G.H. acknowledges support from the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Materials Sciences and Engineering Division under Contract No. DE-AC02-05-CH11231 (Materials Project Program No. KC23MP). The Belgian authors acknowledge computational resources from supercomputing facilities of the University of Liège, the Consortium des Equipements de Calcul Intensif (Grant No. FRS-FNRS G.A. 2.5020.11), and Zenobe/CENAERO funded by the Walloon Region under Grant No. G.A. 1117545. M.C. and O.G. acknowledge support from the Fonds de Recherche du Québec Nature et Technologie (FRQ-NT), Canada, and the Natural Sciences and Engineering Research Council of Canada (NSERC) under Grant No. RGPIN-2016-06666. The implementation of the libpaw library (M.T., T.R., and D.C.) was supported by the ANR NEWCASTLE project (Grant No. ANR-2010-COSI-005-01) of the French National Research Agency. M.R. and M.S. acknowledge funding from Ministerio de Economia, Industria y Competitividad (MINECO-Spain) (Grants Nos. MAT2016-77100-C2-2-P and SEV-2015-0496) and Generalitat de Catalunya (Grant No. 2017 SGR1506). This work has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation program (Grant Agreement No. 724529). P.G. acknowledges support from FNRS Belgium through PDR (Grant No. HiT4FiT), ULiège and the Communauté française de Belgique through the ARC project AIMED, the EU and FNRS through M.ERA.NET project SIOX, and the European Funds for Regional Developments (FEDER) and the Walloon Region in the framework of the operational program “Wallonie-2020.EU” through the project Multifunctional thin films/LoCoTED. The Flatiron Institute is a division of the Simons Foundation. A large part of the data presented in this paper is available directly from the Abinit Web page www.abinit.org. Any other data not appearing in this web page can be provided by the corresponding author upon reasonable request.Peer reviewe

Data from: Standing chromosomal variation in Lake Whitefish species pairs: the role of historical contingency and relevance for speciation

The role of chromosome changes in speciation remains a debated topic, although demographic conditions associated with divergence should promote their appearance. We tested a potential relationship between chromosome changes and speciation by studying two Lake Whitefish (Coregonus clupeaformis) lineages that recently colonized postglacial lakes following allopatry. A dwarf limnetic species evolved repeatedly from the normal benthic species, becoming reproductively isolated. Lake Whitefish hybrids experience mitotic and meiotic instability, which may result from structurally divergent chromosomes. Motivated by this observation, we test the hypothesis that chromosome organization differs between Lake Whitefish species pairs using cytogenetics. While chromosome and fundamental numbers are conserved between the species (2n = 80, NF = 98), we observe extensive polymorphism of subtle karyotype traits. We describe intrachromosomal differences associated with heterochromatin and repetitive DNA, and test for parallelism among three sympatric species pairs. Multivariate analyses support the hypothesis that differentiation at the level of subchromosomal markers mostly appeared during allopatry. Yet we find no evidence for parallelism between species pairs among lakes, consistent with colonization effect or postcolonization differentiation. The reported intrachromosomal polymorphisms do not appear to play a central role in driving adaptive divergence between normal and dwarf Lake Whitefish. We discuss how chromosomal differentiation in the Lake Whitefish system may contribute to the destabilization of mitotic and meiotic chromosome segregation in hybrids, as documented previously. The chromosome structures detected here are still difficult to sequence and assemble, demonstrating the value of cytogenetics as a complementary approach to understand the genomic bases of speciation

Power Spectrum of Acceleration and Angular Velocity Signals as Indicators of Muscle Fatigue during Upper Limb Low-Load Repetitive Tasks

Muscle fatigue is a risk factor for developing musculoskeletal disorders during low-load repetitive tasks. The objective of this study was to assess the effect of muscle fatigue on power spectrum changes of upper limb and trunk acceleration and angular velocity during a repetitive pointing task (RPT) and a work task. Twenty-four participants equipped with 11 inertial measurement units, that include acceleration and gyroscope sensors, performed a tea bag filling work task before and immediately after a fatiguing RPT. During the RPT, the power spectrum of acceleration and angular velocity increased in the movement and in 6–12 Hz frequency bands for sensors positioned on the head, sternum, and pelvis. Alternatively, for the sensor positioned on the hand, the power spectrum of acceleration and angular velocity decreased in the movement frequency band. During the work task, following the performance of the fatiguing RPT, the power spectrum of acceleration and angular velocity increased in the movement frequency band for sensors positioned on the head, sternum, pelvis, and arm. Interestingly, for both the RPT and work task, Cohens’ d effect sizes were systematically larger for results extracted from angular velocity than acceleration. Although fatigue-related changes were task-specific between the RPT and the work task, fatigue systematically increased the power spectrum in the movement frequency band for the head, sternum, pelvis, which highlights the relevance of this indicator for assessing fatigue. Angular velocity may be more efficient to assess fatigue than acceleration. The use of low cost, wearable, and uncalibrated sensors, such as acceleration and gyroscope, in industrial settings is promising to assess muscle fatigue in workers assigned to upper limb repetitive tasks

Macrogen_sequence_files

File produced during the sequencing of the PCR products used for FISH of 5S and 28S rDNA. File names contain "5S" or "28S" depending on what product they refer to

FISH_rDNA

FISH_rDN

Giemsa

Giems