The NanoSCAPE project aims to develop a new analytical methodology based on the use of nanoparticles and spectrometry techniques for the very high sensitive detection of bacteria and pathogens. The use of spectrometrically revealed nanoparticles will allow the direct detection of bacteria with extremely low detection limits, of the order of 0.1 bacteria/ml in biological fluids (e.g. blood, urine, synovial fluid). Furthermore, this approach will allow the highly selective detection and counting of up to 30 strains of target bacteria and pathogens simultaneously and in just a few minutes. As part of the NanoSCAPE project, we will carry out a proof of concept on 10 different strains of bacteria. This new approach could be complementary or even alternative to indirect diagnostic methods such as those based on antibody detection (ELISA, Western blot), or PCR. An application for the direct detection of Borrelia involved in Lyme disease, which is considered difficult to diagnose, will be developed using blood, urine or synovial fluid samples. Through a diagnostic programme on nearly 450 patients (including controls) at different stages of the disease, we will evaluate the NanoSCAPE analytical approach in terms of efficiency, selectivity and ease of implementation on the different biological fluids mentioned above. The results will be systematically compared to existing tests and will allow us to decide on the relevance of proposing new tests based on the methodology developed in the project. Given the wide range of scientific and technological fields involved (analytical chemistry, physical chemistry of nanoparticles, immunology, medicine), we have set up a consortium of 3 public research laboratories (including a university hospital), each of which is an expert in a key discipline, a private company that is a leader in the development of antibodies and a hospital that is recognised as a centre of competence for Lyme disease. A significant part of the project will be devoted to technological (patents with the support of a regional SATT) and scientific (conferences, peer-reviewed articles) development. As such, it is not possible to give more strategic, technical and scientific information on the NanoSCAPE project in this summary. In addition, after having carried out the main actions of technological valorisation, we will boost the interactions towards the general public through several conferences, interventions in high schools/colleges, diffusion on social networks and creation of a comic strip. We will also subcontract an expert organisation in the field of scientific popularisation to ensure not only the quality and content of the media (videos, comic strip) but also high visibility (several million views per week). An association (at least) on Lyme disease will also serve as a relay for the dissemination of the project's progress to the general public. We will also rely on the actions of a competitiveness cluster to help us disseminate our advances to the industrial world. The NANOScape project will thus make it possible to develop a novel, extremely sensitive and rapid approach for the simultaneous detection of bacteria and pathogens in biological fluids, with applications that will ultimately go beyond the detection of Lyme disease.

Brown algae (Phaeophyceae), or brown seaweeds, are multicellular macroalgae that belong to the larger eukaryotic Stramenopile supergroup, which also includes microalgae (e.g., diatoms) as well as heterotrophic protists (e.g., oomycetes). Like plants and animals, brown algae are one of the small number of lineages that evolved complex multicellularity. Yet, the evolutionary process leading to multicellularity in brown algae has been quite distinct, leading to the acquisition of some unique characteristics which are absent in the other lineages. This project aims to deepen the understanding of the molecular processes underlying brown algae development and acquisition of multicellularity through an analysis of the functional regulatory roles of long non-coding RNAs (lncRNAs), key actors in cellular regulation across the Eukarya domain of life. It will employ a multidisciplinary approach, for which the three partners involved have demonstrated expertise, involving comparative genomics and trancriptomics, computational biology, functional biology and epigenomics to characterize how lncRNAs control gene expression programs that define distinct development states in brown algae. Ectocarpus sp. and Saccharina sp. will be used as preferred model systems since they show distinct developmental morphologies but are evolutionary close. On a fundamental level, the BrownLincs project will provide new knowledge on brown algal development regulation and acquisition of complex multicellularity. On a more applied level, this project has the potential to provide novel molecular tools to enable the engineering of high biomass production in brown algae that can be explored to produce new generation, added value materials for food, feed and other industrial applications, in a blue economy context.

SCIENTIFIC CONTEXT. Unicellular organisms need to adapt to rapid and unanticipated changes in their environment. Spores ensure their survival by encapsulating the genome in a protective configuration while awaiting optimal growth conditions. Indeed, yeast spores enter into a quiescent state with minimal metabolic activity and are surrounded by a thick protective wall. Yet, protecting the integrity of the genome in these conditions involves not only a dramatic decrease in transcriptional activity, an extreme nuclear compaction, but also the capacity to completely revert these processes to allow germination. The mechanisms involved in the establishment of genomic quiescence in spores, the protection of their genome and its reactivation, remain unknown. OBJECTIVE. Several lines of evidence show that chromatin is highly compacted in spores. In addition, histone H4 is hyperacetylated and this modification is essential for spore viability. This observation seems counter-intuitive because H4 acetylation (H4ac) is usually associated with transcription activation and open chromatin. Therefore, the general objectives of this project are to understand (i) the mechanisms by which H4 is hyperacetylated in spores, (ii) how H4ac is compatible with quiescence in spores and their chromatin compaction, (iii) whether and how H4ac prepares genome reactivation observed during early germination. IMPACT. Through EpiSpores, we will improve our general knowledge on H4ac signalling pathways, chromatin organisation and transcription regulation. Furthermore, yeast spores provide an alternative model system to investigate the molecular mechanisms of quiescence entry, maintenance and exit in all eukaryotic cells. Finally, our previous work on yeast spores has been translated to the treatment of fungal infections, collectively responsible for 1.5 millions of deaths per year. Our future work exploring chromatin signalling pathways in Candida albicans and their functional role in the virulence of this pathogenic yeast will be based on the technological development of this proposal. CONSORTIUM. This project brings together young researchers, by academic standards, with collective and synergetic expertise in yeast biology, genetics, biochemistry, interactomics, high-throughput genetics, super-resolution microscopy and epigenomic approaches.

Optical microscopy, through its variegated modalities, is an unparalleled approach to investigate the living. Beyond the bare acquisition of a snapshot, it is routinely used to gain a dynamical view of biological processes at a high frame rate (tens of frames per sec.). On top of that, it uses light as a perturbation, to either locally photo-switch the dyes to investigate the dynamics of labelled proteins, or to create a subcellular laser nano-ablation and observe how the biological system cope with it. In industrial setups, high content screening is often limited to bare observation since no generic system can perform photo-perturbative methodologies autonomously. They are still crafty approaches requiring experts; their automating is yet to be done, meaning that they are not usable in screening or routine. The smart autonomous microscopy (SAMic) project aims to open this perspective. We assert that semantic segmentation using fully convolutional network (FCN) as user-customizable image processing, embedded onto an ARM-based dedicated electronics, will enable the real-time processing to detect the right time and place to apply a perturbation (fluorescence switching or nano-ablation), and together with our Inscoper control module, a timely adapting of microscope driving. To tackle these challenges, we will pursue three objectives: (i) Applicative, by developing two experimental biology approaches for which the SAMic is mandatory to drive the developments. The investigated biological questions are current in our labs: the role of AurkA at mitochondria affecting mitochondrial dynamics and the mechanical based robustness of cell division in human cells. (ii) Technological by designing the smartCam-LEAD module (Localised Events Advanced Detector). The main innovation lies in porting a convolutional network powered semantic segmentation to a dedicated ARM-based microprocessor in perspective to achieve real-time, building on our current achievement of machine learning image classification. We will connect it to the microscope driving module to perform autonomous experiments. (iii) Prototype to demonstrate the power of SAMic. We aim here to go beyond a development setup that can only address our two biological questions. Taking advantages of the experience of the consortium in tech development transfer to imaging facilities and the market, we will bring our setup to a proper prototype, appropriate for dissemination by the industrial partner. This involves, in particular, the design of proper HMIs by the industrial partner and the transfer of the prototype on the MRic microscopy facility. The partners teaming up to create the SAMic, two academic labs from IGDR and Inscoper company, have broad expertise, from mathematics for image analysis to microscopy applied in biology through computer science, electronics and instrumental development. These interdisciplinary skills are a distinctive trait of our consortium and, we believe, a strong force to succeed in the project. The SAMic project aims to be a technical and methodological major breakthrough in fluorescence microscopy to investigate life mechanisms which will allow obtaining a large amount of unsupervised photo-perturbative experiments. Artificial Intelligence applied to fluorescence microscopy will dramatically help the researchers to better observe and understand what happens within their live samples. The industrial partner Inscoper aims to offer to the market an interoperable and optimised platform to control any microscopy device and to achieve any image acquisition modalities. Adding the AI and feedback control capabilities will position SAMic as a real disruptive product in the market. Creating an intelligent microscope is one of the next big challenges for the life sciences. The project SAMic will contribute to making it real.