The DyCTheMS project proposes a new experimental approach to the conformational dynamics and thermodynamics of micro-solvated biomolecules, based on ion mobility spectrometry (IMS) and mass spectrometry (MS). The thermodynamics of structural transitions in those systems will be probed using an original calorimetry technique based on IMS measurements. Complementary temperature-dependent isomerization dynamics data will also be collected from tandem-IMS measurements. An originality of the proposal lies in the attempt to bridge the gap between solution and gas-phase measurements by probing how the conformational landscape of a molecular system is modified upon solvation. In particular we will shed light on the extent of solvation required for a biomolecule to exhibit “native” conformational properties. After a validation phase on well-characterized systems, the above procedures will be used to gain insight in the binding-induced structuration of an intrinsically disordered peptide.

Aquatic ecosystems are persistently exposed to environmental stressors such as chemical micropollutants from natural environment or anthropogenic activities. These chemical contaminations may result in alterations of the internal biochemical homeostasis of the aquatic organisms, noticeable at the omics scale. The major limitation in the mechanistic knowledge of environmental chemical toxicity effects on aquatic organisms is the absence of molecular information notably at the genome wide scale in environmentally relevant species. The “omics” technologies – Transcriptomics, Proteomics, Lipidomics, Metabolomics to name a few – offer great promises to help to elucidate molecular responses to exposures in aquatic organisms during specific and vulnerable life cycle stages. Lipid metabolism is the major fundamental metabolic pathway producing energy in animals. In crustacean, lipids play a pivotal role in vulnerable stages like molting, reproduction, development. Recently, it has been shown that chemical compounds interfering with lipid metabolism, recognized as obesogens like tributyltin, mislead the distribution and the synthesis of lipids in the non-target and model organism Daphnia magna. Moreover, pharmaceutical drugs used for hypercholesterolemia to lower cholesterol and triglycerides concentrations like pravastatin or bezafibrate have been detected in sewages. Another study showed that simvastatin exposure in the amphipod Gammarus locusta disturbed the reproduction and population growth at the ng/L range. To understand and predict the effects of toxic exposures, it is crucial to identify the affected metabolic networks. Statins are among the most broadly used pharmaceuticals worldwide and is therefore of emerging environmental concerns. This medication inhibits selectively the enzyme 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMG-CoA reductase) involved in the synthesis of mevalonate, a precursor of sterols including cholesterol. We hypothesize that lipid metabolism may turn out to be the drug-induced toxicity target in aquatic species. However, we are facing a lack of crucial knowledge about the relationships between the abundance of lipid species, the activation/inhibition of signaling and/or biosynthesis pathways and the observed phenotypes. The project PLAN-TOX aim to gain a mechanistic understanding of toxic effects of hypolidiaemia drugs (statins and fibrates) on the sentinel organism G. fossarum. We are proposing to develop and apply an innovative multi-omics approach in ecotoxicology, including (i) the functional proteome and lipidome mapping in the sentinel organism G. fossarum before and after exposure, (ii) the development of methods for the integrative analysis of multi-omics data. G. fossarum is a widely developed sentinel species in ecotoxicology or environmental monitoring and is one of the ecologically relevant species for which we can evaluate the toxicity on different development stages and reproductive cycles. This project will allow to better understand molecular plasticity of energetic metabolism and to identify proteins and lipids involved in physiological changes/responses related to exposure.

Brown and beige adipocytes can generate heat from chemical energy, independently of canonical thermogenesis processes. These adipocytes feature a creatine-based adaptive thermogenesis process activated not only after short-term cold response and long-term cold acclimation, but also possibly by diet. Spiegelman and collaborators have recently proposed, in 2 articles published in nature in 2021, a mechanism based on the futile cycling of creatine phosphorylation and dephosphorylation in the mitochondrial intermembrane space that explain this adaptative thermogenesis capacity. The authors propose that this creatine futile cycle (CFC) relies on two enzymes that catalyze opposite reactions, leading to the dissipation of chemical energy as heat: the B-type creatine kinase (BCK) transfers energy from ATP to produce phosphocreatine, and the tissue-nonspecific alkaline phosphatase (TNAP) hydrolyses phosphocreatine to liberate creatine, that can cycle back to creatine kinase, and heat. This topic of adaptative thermogenesis has gained substantial interest over the last 10 years as it opens critical therapeutic strategies to target obesity and metabolic diseases. Before a potential use of such thermogenesis for therapeutic interventions, a detailed molecular and quantitative understanding of the CFC is required. In this project, ThermoCreatine, recognized experts on molecular components and mechanisms of the CFC join their efforts to dissect the molecular details of the enzymatic and heat generation capacity of the CFC using a range of state-of-the-art biophysical, structural and biological methods. By synergizing the highly complementary and interdisciplinary expertise of this research consortium, we expect to to precisely assess the proposed CFC in vivo and in vitro, evaluate its functioning, relevance and impact in comparison to other thermogenesis mechanisms, and facilitate rational drug design and functional studies.

In the agronomy, the increasing number of reports in the field of plant-bacteria-fungi interactions provides more and more knowledge concerning the nature and function of the microbial communities of the rhizosphere (the microbiome). These plant-microorganisms interactions can be, for a large part, linked to microbial secondary metabolites secreted by these microorganisms, but numerous ones are not yet characterized. Studies of the direct use of bacteria in agronomic formulations will not be targeted by this study, it is the secondary metabolites by particular bacteria that will be our focus. The following reasons have guided this choice: - (i) An environmental and societal need prompts us to produce pesticide-free food and the increased market demand for greater quantities of food. - (ii) The bacteria selected in this study showed an effective agronomic effect to stimulate the plants and were not studied for the applications envisaged in this project. - (iii) Replacing existing agronomic formulations by products based on the secondary metabolites responsible for activities with improved efficiency while respecting the environment. - (iv) The chemical variety of the secondary metabolites produced by these bacteria prompts us to evaluate them for pharmaceutical activities (example resistance cases). This task can provide a major opening to future pharmaceutical development projects. The production of secondary metabolites from bacteria (Agronutrition) and extraction, fractionation and identification of molecules (LGC-pharma) have already been performed on two models bacteria (Burkholderia sp. and Bacillus megaterium) as part of a collaborative thesis (Belkacem MA, 2016). The work was focused on low volatile extracts followed by the identification by GC-HRMS. One hundred molecules have been identified and twenty of them have been cited in the literature for the first time. This early original results have encouraged us to expand the work with other partners, with other goals and other microorganisms. Pharmaceutical activities (antioxidant, antimicrobial and cytotoxic) were chosen following interesting activities obtained during the thesis work of M Belkacem MA. The objective of VAMAGPHAR is to identify and develop secondary bacterial metabolites that can be used in agriculture as Biostimulants and/or pharmaceutical treatment as a new source of biologically active molecules, to answer questions of public health indirectly (agriculture) by substituting the input of chemical fertilizers and pesticides or directly (pharmaceutical). This requires a large interdisciplinary cooperation between different specialists (collaboration with private companies): agronomists, microbiologists, chemists and biochemists to obtain the innovative products. The overall initial methodology proposed in the VAMAGPHAR project to achieve these objectives includes the following key steps: (i) production of secondary metabolites from soil bacteria, they are effective for the growth of plants and not studied (Streptomyces beta-vulgaris, Burkholderia sp., Pseudomonas putida, Paenibacillus sp, Ochrobactrum sp., Enterobacter ludwigii and Bacillus mucilaginosus). (ii) optimization and identification of chemical composition of volatile compounds (on-line and by trapping on adsorbing phase), (iii) extraction, evaluation of the agronomic and pharmaceutical activities and bioguided fractionation of interesting extracts to isolate the active substances. (iv) process optimization production of the extracts and/or active molecules, (v) develop formulations from active molecule or extract in the agronomic and in vivo fields for the pharmaceutical (preliminary) activities. A multidisciplinary research consortium gathering analytical chemistry (LGC-pharma), identification of volatiles compounds (ISA), production process of secondary bacterial metabolites (LGC-process) and 2 companies (Agronutrition & Explorair) was thus built.

Modern societies increasingly rely on goods and services provided by subterranean ecosystems for their well-being and development. Ground water is increasingly being extracted for drinking water supply to accommodate the world population growth and surface water pollution. Alternative water management practices such as the intentional stormwater infiltration developed in urban areas can increase groundwater recharge. However, the environmental efficacies of such kind of managed aquifer recharge (MAR) practices rely exclusively on the self-purification capacity of soils and aquifers. Although the performance of MAR systems to prevent groundwater contaminations by hydrocarbons and heavy metals has been demonstrated, it is not the case for chemicals like pesticides/biocides and microbes including bacterial pathogens. Moreover, MAR practices generate major physical (temperature fluctuations) and chemical (oxygen content decrease) disturbances for groundwater ecosystems. Nevertheless, studies on the functional response of groundwater ecosystems to these disturbances are lacking. What is the resistance and resilience of these ecosystems to disturbances? Are groundwater microbial communities that play key roles in water purification processes vulnerable to these disturbances? The present project aims to fill these gaps through field and laboratory experimental approaches. Research will be developed along four closely related tasks. The workpackage (WP) 1 will be partly devoted to the development of sampling tools based on integrative samplers to evaluate groundwater microbial diversity but also the transfer of bacterial and chemical contaminants from surface water to groundwater in MAR systems (Actions 1.1 and 1.2). The WP 2 will focus on the hydrogeological modelling of the water transfer in 6 MAR systems presenting contrasted physical characteristics (vadose zone thickness, hydraulic conductivity of the infiltration bed of the basin,…) (Action 2.1) and the coupling of this modelling approach with chemical and biological contaminant transfers during three stormwater events (Action 2.2). Such coupling will allow a precise description of the plume of stormwater in groundwater, its potential impact on water quality, and the contribution of MAR system characteristics to contaminant transfers. The WP 3 will quantify the functional responses of local groundwater microbial communities to disturbances associated with MAR practices. Based on a coupling of field (Action 3.1) and laboratory (Action 3.2) works, the structural and functional resistance and resilience of groundwater microbial communities will be assessed during disturbances generated by stormwater events. The results of the project will contribute to the definition of recommendations for stormwater infiltration device design and for operational monitoring systems. WP 4 focuses exclusively on the transfer of scientific research to the management of stormwater infiltration in urban areas. All these tasks will contribute to increase our knowledge on the functioning of groundwater ecosystems and their responses and vulnerabilities to urban-impacted conditions. Development of integrative samplers is a crucial initiative to evaluate the occurrence of chemical and biological contaminants present at low concentrations in groundwater. It will allow the first quantification of MAR system performances on groundwater quality. Our project also has the ambition to develop functional indicators of groundwater ecosystem health intended for water managers.