By limiting the impact of DNA damage, DNA repair systems play a critical role in cell survival and the avoidance of mutations leading to pathologies such as neurodegenerative diseases, cancer, and accelerated aging. We have recently shown that in response to oxidative stress, the co-transcriptional regulator Mediator complex is essential for the chromatin recruitment of OGG1, the DNA glycosylase that initiates base excision repair (BER) of the mutagenic 8-oxoG lesion. During the last few years, a new exciting view has emerged suggesting that 8-oxoG is not only a DNA lesion that challenges the stability of our genomes but could also be considered an epigenetic mark playing a major role in transcriptional activation. Most of our knowledge regarding the mechanisms underlying the search and cleavage of 8-oxoG by OGG1 comes from in vitro experiments on 8-oxoG containing naked DNA but very little is known about the impact of the chromatin state on these processes. Our project aims to fill this gap by assessing directly in living cells and at the single molecule resolution the dynamic behavior of OGG1 and the Mediator complex upon oxidative stress. Our findings will shed light on the complex interplay between repair and transcription, two processes that appear to be intimately connected according to an ever-growing number of evidences. Assessing the search strategies employed by OGG1 to detect 8-oxoG lesions within the nucleus will also bring new concepts beyond the DNA repair field by showing how proteins navigate within the highly complex nuclear environment and find their target with high efficiency and specificity.

Small ruminant production systems are a major component of the dairy and meat sector in the Mediterranean region, being frequently the only possible enterprises in less favoured areas, unsuitable for growing crops, playing a substantial role in the agro-livelihood of farmers in developing countries. Thus, it is fundamental to ensure sustainability and prevent diseases in grazing sheep systems. Parasites are ubiquitous in such systems and have been identified as the main constraint affecting small ruminants’ production, health and welfare. Among parasitic infections, cystic echinococcosis (CE) is one of the most important production-limiting diseases of grazing sheep in the Mediterranean area, associated to serious animal health, welfare and economic repercussions due to reduced yield and quality of meat, milk and wool, reduced birth rate and delayed performance and growth. CE is caused by the larval stages of the small tapeworm Echinococcus granulosus, a zoonotic Taeniidae of veterinary and public health importance. The life cycle of E. granulosus includes dogs and other canids as the definitive hosts of the adult parasite and livestock (mainly sheep) and humans as intermediate hosts. CE has a worldwide distribution, but it exhibits the highest prevalence in communities where pastoral activities predominate, as the Mediterranean area. Climatic changes (e.g. precipitation, climate warming) may influence the epidemiology of CE, due to their direct effect on the survival of infective eggs, released in the environment by the dog and an indirect impact on sheep, through an increased exposure to the parasite. For these reasons, the ECHINO-SAFE-MED project is aimed to implement the farming systems by delivering innovative and sustainable strategies to control CE in sheep in four countries of the Mediterranean area (Algeria, Greece, Italy and Tunisia). The aims and objectives will be achieved thanks to 5 inter-linked Work Packages (WP). The WP1 aims to develop and harmonize innovative tools for the early diagnosis of CE in sheep (ultrasound technique, sandwich-ELISA and skin test) to be transferred and applied, afterwards, in the surveillance and control activities in the farming systems and hub laboratories of endemic Mediterranean areas. In WP2, CE surveillance activities will be improved in pilot areas in order to obtain a baseline level of (cystic) echinococcosis infection in definitive (dogs) and intermediate (sheep) hosts. The results obtained will be used to select sheep farms in which sustainable control strategies will be performed (WP3). Specifically, three different control strategies, based on a different combination of vaccination of lambs and treatment of dogs, will be tested to reduce the level of parasite transmission. Furthermore, an innovative strategy based on praziquantel-laced baits delivered by drones will be used to treat stray dogs or other canids present in grazing areas identified through the points tracked by animal movements using GPS dataloggers (WP2). Capacity building and training activities will be conducted to secure adequate expertise within surveillance and control measures for CE, and the methods and tools applied throughout the project; furthermore, the outcomes of WP1-3 will be disseminated to endusers, stakeholders and authorities to strengthen CE control capacity (WP4); finally, WP5 will be devoted to project management. The objectives will be achieved through the construction of an international network (eight partners) for sharing practices, methods and data to promote in concerted and organized way, efficient approaches to help animals and farming systems to adapt to climate change. Re-designing diagnostic tools and control strategies will increase the resilience of Mediterranean farming systems to increased disease risks arising from global change and will produce yield stability and quality in comparison to standard control approaches under challenging environmental conditions.

This project focuses on technological and methodological developments in cryo electron microscopy (cryo-EM) for structural biology, through the development of methods and software for the rapid determination of complete sets of all-atom conformations (all-atom conformational landscapes) of biomolecular complexes from cryo-EM images. Building upon the results of our established consortium, we will develop a unified and rapid methodology (and the corresponding software) that combines advanced approaches to image analysis, molecular dynamics simulation and artificial intelligence (deep learning), which will enable rapid and comprehensive determination of atomic conformational landscapes from cryo-EM images. The determination of the entire set of all-atom structural models, from millions of cryo-EM images of a biomolecule in interaction with other molecules (ligands, drugs), will have great impact on structure-based drug discovery. These developments will be tested and applied to two biomedically important macromolecular complexes exhibiting notable flexibility in the context of their binding factors related to protein synthesis (the human 80S ribosome) and protein degradation (the human ATPase p97). This will enable detailed structural analyses of these complexes and improve our understanding of the molecular mechanisms of their binding with factors, as well as their functions and dysfunctions. Furthermore, this work will serve as a reference to others aiming at obtaining all-atom conformational landscapes of large macromolecular complexes like the human ATPase p97 (~37 000 atoms) and the human 80S ribosome (~250 000 atoms), which is unamenable to classical cryo-EM image processing methods. The new developments (methods and software codes) will be applicable to any biomolecule that can be analyzed by cryo-EM.

Urbanization completely disturbs the water cycle, through the creation of impervious surfaces which reduce infiltration and massively increase stormwater runoff volumes. With urbanization set to increase, and uncertainty due to climate change impacts, there is a critical and internationally recognized need to increase the permeability of the urban landscape and to restore a more natural water cycle in cities. However, due to the contamination of urban surfaces, runoff water may carry high concentrations of pollutants. Where infiltration is used to mitigate stormwater runoff, this can result in the transfer of pollutants into urban soils and the water table, which poses the question of pollution of groundwater and surface water. Urban soils should be checked regarding their capability to infiltrate water, at the same time as promoting the filtration of pollutants. INFILTRON therefore aims to develop a large ring infiltrometer for evaluating the infiltration & filtration functions of urban soils. The innovative aspects of the project are (i) the development of tracers specifically for emerging pollutants and bacteria, detectable using non-invasive techniques (MRI – magnetic Resonance Imaging for laboratory experiments and GPR – Ground Penetrating radar for field), (ii) the size of the device for addressing the appropriate spatial scales for accounting for preferential flow and mass transfer that often establish in urban soils as the result of their strong heterogeneity, (iii) the development of a methodology and a functional "all-in-one" tool combining the experimental device and a numerical model specifically designed to be user-friendly for use by practitioners and engineers. This tool will allow a quantitative measurement of the infiltration & filtration functions of urban soils, which is of great interest to managers of infiltration systems / bio-retention ponds, but also of polluted sites and soils. To disseminate the results as widely as possible, the consortium will produce an industry-focused guide for the use of the INFILTRON package (with supporting technical reports), build a specific website for online data access, design a commercial strategy for INFILTRON package dissemination and will organize a technical workshop, open to stakeholders, consultant engineers, managers of infiltration systems and polluted sites, and regional and local authorities. The consortium will also ensure an active publication policy in peer-reviewed journals, including high rank open source scientific publications and participation in major international conferences (e.g. EGU, NOVATECH, AGU, WCSS), along with a specific conference on the topic of preferential flow and mass transfer in urban soils to be hosted by EGU and on the management of stormwater and runoff water in the city to be hosted by NOVATECH. In summary, the consortium will deliver knowledge, design guidance and practical tools to support the market for stormwater eco-technologies for the mitigation of urbanization impacts on the water cycle, soil and groundwater quality. The consortium will benefit from committed partnerships with an internationally well-recognized Australian research team in the field of stormwater infiltration systems and with an internationally well recognized Italian team in the field of infiltration measurements.