Many imaging techniques, particularly in environmental transmission electron microscopy (ETEM), generate images with degraded signal-to-noise ratio, contrast and spatio-temporal resolution, which hamper quantification and reliable interpretation of data. Moreover, the extraction of structural information from these images relies on manual acquisition and local structural identification which does not allow statistical analysis of the data and necessarily introduces a human bias carried out at the post-processing stage. The general aim of the ARTEMIA project is to develop a ground-breaking deep learning-based framework for in situ microscopy in liquid and gaseous media allowing the automated, high throughput, real-time acquisition and analysis of ETEM image sequences.Our framework will integrate aberration-corrected in situ ETEM imaging using windowed liquid/gas nanoreactors with denoising and resolution enhancement scheme set up using convolutional neural network (CNN). For model training, datasets consisting of simulated liquid- and gas-phase TEM images will be generated by by atomistic simulations including instrumental noise and imperfections of the microscope optics. In the ARTEMIA project, the CNN models will be applied to the study of two crystalline samples with complementary structural characteristics and electron beam sensitivity, model gold nanoparticles (Au NPs) and microporous zeolite, in reactive gas and/or liquid environments. Our scientific aim will be to gain further mechanistic understanding ofthe growth of model Au NPs in liquid phase and their reactivity in oxidizing and reducing gas environments on one hand and the steaming process of beam-sensitive zeolite on the other hand. The consortium comprises three academic partners (MPQ, LEM, IPCMS) and an EPIC partner (IFPEN) with complementary expertise in liquid and gas ETEM, data science and image processing with special focus on deep learning approaches, atomic modelling and TEM image simulation.

Ribonucleoprotein particles (RNPs) are made of RNA associated with proteins and play a central role in biological systems (maintenance of cellular homeostasis, establishment of infectious or pathological processes). The identification of the components of these RNPs has exploded over the past decade thanks to the use of high-throughput analytical approaches. The fine characterization of the interaction of the components of these RNPs then requires the analysis of a large number of mutants. While several high-throughput methodologies have been developed for the analysis of RNA mutant libraries, progress has been scarcer on the protein side. To fill this gap, we propose "SURF", a highly multidisciplinary project aiming at developing a new chemistry for the efficient capture of target RNAs on the surface of water-in-oil droplets produced, manipulated, and analyzed at rates of several million per hour in microfluidic devices. Gene libraries encoding mutants of the studied protein fused to a fluorescent domain will be expressed in vitro at a rate of one mutant (produced in large numbers of copies) per droplet. Thus, a mutant able to interact with the target RNA sequence will lead to a relocation of the fluorescent protein on the surface of the droplet, making it easily discriminable from a drop containing a mutant unable to recognize its target (fluorescence remaining diffuse in the droplet). Applied and validated with various biological models, this technology will not only allow to finely characterize the formation of RNPs, but also to reprogram their specificity, and even to identify molecules able to modulate this interaction. Finally, this project will also be an opportunity to explore surfactants made of alternative chemistries having a lower impact on the environment.

ANG-G: The geo-localization of a digital archive: the Gaignières Collection The main objective of the ANG-G project is to create an interface that will allow the exploratory cartography of one of the richest documentary collections ever assembled concerning the medieval and modern history of families, territories and European patrimony. The Gaignières Collection, housed mainly at the Bibliothèque nationale de France and the Bodleian Library in Oxford, is the work of a single man whose methods of research and classification offer a totally new vision of the history of patrimony embedded within its territory, just as the Age of Enlightenment is dawning. Both a traveler and a scholar, Gaignières had the fundamentally new idea of making an archival, archaeological, artistic and sociological inventory of France within a European perspective. He even extended his enquiry to China. For forty years, aided by his draftsman Louis Boudan and his scribe-palaeographer Barthélemy Rémy, he set down on paper copies of charters and drawings of monuments and surrounding landscapes, intent on describing a world that would disappear. By so doing, Gaignières has handed down to us an instantaneous portrait of 17th-century France and, more systematically, northern France (thousands of texts and over 7500 drawings). While he personally explored the Capetian territories of northern France, he created networks of scholars and acquired books, manuscripts and engravings concerning the southern French provinces and foreign realms. As the Englishman Martin Lister would note with wonderment in 1698, “He has all of Europe arranged in categories.” Fortunately his legacy has escaped the ravages of a Revolution and two world wars. An inspired archivist, Gaignières invented a system of classification that conformed to his encyclopedic vision of history and its relationship to territory. By making several identical copies to be filed in his different dossiers on topography, institutions, families, heraldry, costume, etc., and by using cross-references, he was able to create new relationships and vary the scale of observation, thus breathing life into the documentation. Such a documentary procedure, one that carves, structures, and interlinks open and evolving fields, confers on the textual copy or drawing a meaning that is never unequivocal or exclusive. In a word, his collection is original to the point of anticipating in many respects today’s computer databases. Although this exceptional collection was dismantled after the death of the antiquary and dispersed in the different departments of the Bibliothèque nationale and the Bodleian Library, Oxford, the original early 18th-century inventories have enabled its virtual reconstruction on a special website, Collecta. Archive numérique de la collection Gaignières. Having recaptured a total vision of the collection with the website, the ANG-G project will now allow us to discover its riches in an entirely new way by offering the possibility of visualizing its texts and objects on ancient or more recent maps by varying the scale of observation, the time-frame, and the criteria of interrogation. The development of the interface by a cross-disciplinary team of historians, art historians, geohistorians and designers, its linkage to the geo-referenced semantic-web platform Oronce-Fine, and the creation of a window for non-scholarly participation will allow a diversified array of scholars and amateurs to re-appropriate this extraordinary collection as a source for research and a vector for the knowledge of regional patrimony, whether still extant or vanished.

Metallic micropollutants are rejected by chemical, mining, electronics and metallurgical industries. They can accumulate into living organisms and thus lead to health problems. Furthermore, regulations become ever more severe on maximum accepted concentration levels on wastewater. The project ESSENTIAL aims to develop an original and efficient continuous flow process using open cell polymer foams coated with a polyphenolic film of bio-based origin to capture and recover toxic metals. Thanks to its elastic feature, the compression of a polymer foam within a given volume should increase the global specific surface available to adsorb more metallic ions and thus increase the competitiveness of this approach. Furthermore, applying cycle of compression-release of the stationary phase during the adsorption or desorption step should intensify both. This strategy contributes to the sustainable management of natural resources, diversify the metals supply and will offer an original, economically competitive and eco-compatible pollution control alternative using a compressible, recoverable and recyclable filtration material.

The new virus discovered in December 2019, is a coronavirus causing an outbreak of pulmonary disease. Its rapid spreading over the world led on March 11, the World Health Organization to declare the outbreak a pandemic. The new coronavirus is a positive single stranded RNA molecule that is immediately translated upon its entry into the cell. The first protein to be translated, NSP1, binds to the host small ribosomal subunit 40S and recruits a yet unidentified cellular nuclease that triggers the degradation of the host mRNAs. In this way, the virus hijacks the host translation machinery to its own and exclusive use. Evidence suggests that an internal ribosomal entry site (IRES), immune to the NSP1 inactivating effect, initiates the COVID-19 RNA translation. The current proposal addresses the molecular mechanisms of translation initiation of the viral RNA during the COVID-19 infectious process. We will focus on the role of the 5’UTR of the viral genome in order to determine whether it uses a novel IRES element and to identify the RNA regions implicated. We will also investigate the function of NSP1 protein and characterize the mode of action of translation inhibition of cellular mRNAs. Overall, the main goal of this proposal is to understand the fundamental mechanism of viral translation during COVID-19 infection in order to develop a functional screen for testing specific inhibitors for therapeutic purposes. In preliminary investigations, we have compared the predicted RNA structure of the 5’UTR of COVID-19 with the IRES structures of HCV and CrPV and predicted its 3D structure (coll. Zhichao Miao, Newcastle University). In 3D structure comparisons, we find internal loops as potential function sites and inhibitory elements that would prevent binding of eIF4E, essential component of the canonical translation initiation machinery. In translation assays we have already showed that translation is essentially mediated by a cap-independent mechanism. In this proposal we will characterize the putative IRES by chemical probing and mutagenesis in order to determine its structure. The binding of human 40S particles will be explored by sedimentation assays on sucrose gradients and the scanning ability evaluated by AUG shift assays. The activity of the IRES variants will be further measured by translation assays of IRES-reporters constructs. Altogether, these assays should lead to a comprehensive understanding of the IRES structure and mechanism of ribosome recruitment. In parallel, the cellular trans-acting factors, such as the unknown nuclease recruited by NSP1, will be identified by Mass Spectrometry analysis using purification protocols developed in the lab to purify huge ribosome-mRNP complexes. Later, we will set up a complete pipeline from the NSP1 gene cloning to the atomic structure of NSP1 in complex with the human 40S ribosomal subunit programmed with the IRES RNA by cryo-EM. As COVID-19 spreading is extremely fast, a protocol based on cell-free translation assay will be immediately implemented for high-throughput screening of drugs that have already been shown to be active on RNA IRES elements as well as against available chemical libraries. We are planning to recapitulate the NSP1-mediated specific inhibition using two reporters, a reporter containing 5’UTR from ß-globin that is targeted by NSP1 and another immune reporter containing the COVID-19 IRES. This will allow isolating specific inhibitors that have exclusive effects on NSP1, namely, the inhibitor should specifically target the COVID-19 and be a potential drug candidate against COVID-19 disease. For this part, we will collaborate with two spin-off companies of the University of Strasbourg, NovAliX and Urania Therapeutics, that have expertise in functional and in silico high-throughput screening techniques.