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Alternative silencing states of Transposable Elements in Arabidopsis associated with H3K27me3
No full textInternational audienceBackground. The DNA/H3K9 methylation and Polycomb-group proteins (PcG)-H3K27me3 silencing pathways have long been considered mutually exclusive and specific to transposable elements (TEs) and genes, respectively in mammals, plants, and fungi. However, H3K27me3 can be recruited to many TEs in the absence of DNA/H3K9 methylation machinery and sometimes also co-occur with DNA methylation.Results. In this study, we show that TEs can also be solely targeted and silenced by H3K27me3 in wild-type Arabidopsis plants. These H3K27me3-marked TEs not only comprise degenerate relics but also seemingly intact copies that display the epigenetic features of responsive PcG target genes as well as an active H3K27me3 regulation. We also show that H3K27me3 can be deposited on newly inserted transgenic TE sequences in a TE-specific manner indicating that silencing is determined in cis. Finally, a comparison of Arabidopsis natural accessions reveals the existence of a category of TEs—which we refer to as “bifrons”—that are marked by DNA methylation or H3K27me3 depending on the accession. This variation can be linked to intrinsic TE features and to trans-acting factors and reveals a change in epigenetic status across the TE lifespan.Conclusions Our study sheds light on an alternative mode of TE silencing associated with H3K27me3 instead of DNA methylation in flowering plants. It also suggests dynamic switching between the two epigenetic marks at the species level, a new paradigm that might extend to other multicellular eukaryotes.</p
Unravelling genomic drivers of speciation in Musa through genome assemblies of wild banana ancestors
No full textData availability: The Illumina, ONT, PACBIO HiFi, Bionano Genomics, Hi-C data, assemblies and annotations generated in this study have been deposited in the European Nucleotide Archive under project PRJEB72282. The genome assemblies and gene and TE annotations are available at Banana Genome Hub [http://banana-genome-hub.southgreen.fr]. GBSS and ADH alignments, EDTA repeat database and LTR repeat database produced are available on the Banana Genome Hub [http://banana-genome-hub.southgreen.fr] in the download section and on CIRAD dataverse [https://doi.org/10.18167/DVN1/6TLMD3]. The GBS data are available in the Short Read Archive under the following projects PRJNA1078411, PRJNA1182927 and PRJNA667853. Germplasm is available at the CIRAD-INRAE Biological Resource Centre for Tropical Plants (CRB-PT) in the West Indies (Guadeloupe, France) for accessions PT-BA-00024 (M. a. ssp. banksii); PT-BA-00228 for M. textilis; PT-BA-00182 for M. a. ssp. zebrina; PT-BA-00051 for M. a. ssp. burmannicoides and PT-BA-00304 for the diploid cultivated Pisang Madu. Germplasm of M. schizocarpa is available at the Bioversity International Transit Center in Leuven (Belgium) under ITC0926 accession number. Publicly available sequencing data (PRJEB58004 [https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJEB58004] and PRJEB26661) were also used in this study. Source data are provided with this paper.Code availability: Custom code has been added to vcfHunter toolbox that is available at Github [https://github.com/SouthGreenPlatform/VcfHunter].International audienceHybridization between wild Musa species and subspecies from Southeast Asia is at the origin of cultivated bananas. The genomes of these cultivars are complex mosaics involving nine genetic groups, including two previously unknown contributors. This study provides continuous genome assemblies for six wild genetic groups, one of which represents one of the unknown ancestor, identified as M. acuminata ssp. halabanensis. The second unknown ancestor partially present in a seventh assembly appears related to M. a. ssp. zebrina. These assemblies provide key resources for banana genetics and for improving cultivar assemblies, including that of the emblematic triploid Cavendish. Comparative and phylogenetic analyses reveal an ongoing speciation process within Musa, characterised by large chromosome rearrangements and centromere differentiation through the integration of different types of repeated sequences, including rDNA tandem repeats. This speciation process may have been favoured by reproductive isolation related to the particular context of climate and land connectivity fluctuations in the Southeast Asian region
Ballada o outsiderach i arywistach
No full textDGP - Dziennik Gazeta PrawnaWe współczesnej Polsce system klasowy istnieje, ma się dobrze i jest prawie całkowicie zabetonowany. Jak dekady temu skonstatował Leonard Cohen, bogaci się bogacą, biedni biedują. Ale przecież chyba nie wszyscy? Nawet w najbardziej skostniałych systemach (a akurat polskiemu społeczeństwu daleko do feudalnych czy kastowych hierarchii społecznych) zawsze zdarzały się jednostki, którym się udawało – dzięki umiejętnościom, szczęściu i ciężkiej pracy (niekoniecznie w tej kolejności) wspięły się ponad swój stan i zostały… No właśnie, kim
Enhancing supply chain resilience with recovery strategies under electricity shortages
No full textInternational audienceElectricity shortages triggered by extreme events have profoundly disrupted supply chains (SCs) in recent years. As SC operations heavily depend on electricity, simultaneous uncertainties may occur in supply and production capacities, demand, and transportation capacity if electric trucks are used. To enhance SC resilience, it is imperative to combine new recovery strategies (i.e. alternative energy sources and alternative transportation vehicles (ATVs)) with traditional ones to restore SC performance. However, these strategies have not been investigated quantitatively. Besides, only partial probability distribution information of uncertainties may be available under electricity shortages. Thus, this work improves SC resilience from a worst-case perspective, where the moment information is known. For the problem, a bi-objective distributionally robust chance-constrained optimisation model is constructed to balance the total cost and the service level. Then, an effective ϵ-model-based constructive heuristic (ϵ-MBCH) is developed. Compared with the ϵ-constraint method, the efficiency of ϵ-MBCH is improved by 99.81%. Based on stress tests and sensitivity analyses on a real case, key managerial insights include: (i) the ATV strategy is indispensable under varying severities of electricity shortages; (ii) the inventory management strategy helps reduce reliance on power generators and diesel trucks; and (iii) mitigating demand variability is essential for reducing costs
XRTwin4Industry: A Comprehensive Framework for Standardisation and Interoperability in XR-Enabled Industrial Digital Twins
No full textInternational audienceThis paper introduces XRTwin4Industry, a comprehensive framework designed to tackle key challenges in the use of Extended Reality for industrial digital twin applications, specifically focusing on visualisation, interaction, standardisation, and interoperability. By conducting a state-of-the-art review, we identify the major obstacles and propose solutions through an integrated methodology that encompasses a tailored data model and system architecture aligned with the IEC 63278 standard series and the Asset Administration Shell vision of Industry 4.0, ensuring compatibility with current industrial standards. To validate this approach, both a Proof of Concept and a real-world application scenario are developed, demonstrating the practical viability of the proposed framework. Additionally, the project is made available as open-source, allowing for community collaboration and further development. The design is further evaluated using User-Centered Design principles to ensure usability and effectiveness in industrial settings
Les livreurs de plateformes en France : risques au travail et protection sociale
No full textThis study report presents a categorisation of food platform delivery workers, a mapping of the French ecosystem in which they operate, an analysis of the economic and health risks they face, and the nature for their social protection. It concludes with recommendations for strategies and public policies to take better care of these vulnerable workers.The results are based on 236 responses to an online questionnaire, supplemented by 18 semi-structured interviews, two non-structured interviews, and several participant and non-participant observations at delivery workers' meetings and public demonstrations in Paris and Lyon. Three complementary publications are available in open access: ‘Young, poor and vulnerable: delivery riders in France are demanding better wages and social protection’ (The Conversation), ‘La tyrannie d'algorithmes ayant pignon sur rue’ (Revue Terminal), ‘Responsible Innovation and Digital Platforms: The Case of Online Food Delivery’ (Journal of Innovation Economics & Management).Ce rapport d'étude présente une catégorisation des livreurs de plateformes de nourriture, une cartographie de l'écosystème français dans lequel ils évoluent, une analyse des risques auxquels ils sont confrontés en matière économique et de santé, et les modalités de leur protection sociale. Il conclue sur des recommandations en matière de stratégies et de politiques publiques pour mieux prendre soin de ces travailleurs vulnérables.Les résultats se basent sur 236 réponses à un questionnaire en ligne, complété par 18 entretiens semi-directifs, deux entretiens non directifs, et plusieurs observations participantes et non participantes dans des réunions et des manifestations publiques des livreurs à Paris et à Lyon. Trois publications complémentaires sont en libre accès : "Les livreurs de plateformes en quête de protection sociale" (The Conversation), "La tyrannie d’algorithmes ayant pignon sur rue" (Revue Terminal), "Responsible Innovation and Digital Platforms: The Case of Online Food Delivery" (Journal of Innovation Economics & Management)
Quand les outils numériques génèrent des expériences négatives au travail
No full textInternational audienceWhy do some employees feel overdigitalized at work and others don't? Far from being an objective phenomenon, overdigitalization corresponds to different contexts and perceptions. As part of my thesis work with the City and Metropolis of Rennes, initial results from the exploratory phase highlighted ten dimensions of over-digitalization.Pourquoi des salariés se sentent sur-numérisés au travail, et pas d’autres ? Loin d’être un phénomène objectif, la sur-numérisation correspond à des contextes et à des perceptions différentes. Dans le cadre de mes travaux de thèse menés avec la Ville et Métropole de Rennes, des premiers résultats de phase exploratoire ont mis en évidence dix dimensions de la sur-numérisation
Étude de comparaisons de procédures de sélection de variables en régression linéaire gaussienne de grande dimension
No full text38 pages, 23 figures, 1 tableWe propose an extensive simulation study to compare some variable selection procedures in a high-dimensional framework. Assuming that the relationship between the actives variables and the response variable is linear, the high-dimensional Gaussian linear regression provides a relevant statistical framework to identify active variables related to the response variable. Many variable selection procedures exist, and in this article, we focus on methods based on regularization paths. We perform a comparison study by considering different simulation settings with various dependency structures for variables and evaluate the performance of the methods by computing several metrics. As expected, no method is optimal for all the evaluated performances but we provide recommendations for the best procedures according to the metric to control. Lastly, we test the importance of some assumptions of the model, especially the high dimensionality and the Gaussian ones
Multiple, diverse endogenous giant virus elements within the genome of a brown alga
No full textInternational audienceEndogenous viral elements (EVEs) have been found in diverse eukaryotic genomes. These elements are particularly frequent in the genomes of brown algae (Phaeophyceae) because these seaweeds are infected by viruses (Phaeovirus) of the phylum Nucleocytoviricota (NCV) that are capable of inserting into their host’s genome as part of their infective cycle. A search for inserted viral sequences in the genome of the freshwater brown alga Porterinema fluviatile identified seven large EVEs, including four complete or near-complete proviruses. The EVEs, which all appear to have been derived from independent insertion events, correspond to phylogenetically diverse members of the Phaeovirus genus and include members of both the A and B subgroups of this genus. This latter observation is surprising because the two subgroups were thought to have different evolutionary strategies and were therefore not expected to be found in the same host. The EVEs contain a number of novel genes including a H4 histone-like sequence but only one of the EVEs possesses a full set of NCV core genes, indicating that the other six probably correspond to nonfunctional, degenerated viral genomes. The majority of the genes within the EVEs were transcriptionally silent and most of the small number of genes that showed some transcriptional activity were of unknown function. However, the existence of some transcriptionally active genes and several genes containing introns in some EVEs suggests that these elements may be undergoing some degree of endogenization within the host genome over time
Global weak solutions for a variation of the Whitham equation
No full textWe study in this article a variation of the Whitham equation which was introduced as an alternative to the KdV equation. We first prove the global existence of weak solutions, then we establish a regularity criterion from which we deduce the uniqueness of weak solutions. Local in time criterions for regularity and uniqueness are also given