Publications

2023

• Light-independent regulation of algal photoprotection by CO2 availability
  
  • Águila Ruiz-Sola M.
  • Flori Serena
  • Yuan Yizhong
  • Villain Gaelle
  • Sanz-Luque Emanuel
  • Redekop Petra
  • Tokutsu Ryutaro
  • Küken Anika
  • Tsichla Angeliki
  • Kepesidis Georgios
  • Allorent Guillaume
  • Arend Marius
  • Iacono Fabrizio
  • Finazzi Giovanni
  • Hippler Michael
  • Nikoloski Zoran
  • Minagawa Jun
  • Grossman Arthur R
  • Petroutsos Dimitris
  Nature Communications, Nature Publishing Group, 2023, 14 (1), pp.1977. Photosynthetic algae have evolved mechanisms to cope with suboptimal light and CO 2 conditions. When light energy exceeds CO 2 fixation capacity, Chlamydomonas reinhardtii activates photoprotection, mediated by LHCSR1/3 and PSBS, and the CO 2 Concentrating Mechanism (CCM). How light and CO 2 signals converge to regulate these processes remains unclear. Here, we show that excess light activates photoprotection- and CCM-related genes by altering intracellular CO 2 concentrations and that depletion of CO 2 drives these responses, even in total darkness. High CO 2 levels, derived from respiration or impaired photosynthetic fixation, repress LHCSR3 /CCM genes while stabilizing the LHCSR1 protein. Finally, we show that the CCM regulator CIA5 also regulates photoprotection, controlling LHCSR3 and PSBS transcript accumulation while inhibiting LHCSR1 protein accumulation. This work has allowed us to dissect the effect of CO 2 and light on CCM and photoprotection, demonstrating that light often indirectly affects these processes by impacting intracellular CO 2 levels. (10.1038/s41467-023-37800-6)
  DOI : 10.1038/s41467-023-37800-6
• Widening the landscape of transcriptional regulation of green algal photoprotection
  
  • Arend Marius
  • Yuan Yizhong
  • Ruiz-Sola M Águila
  • Omranian Nooshin
  • Nikoloski Zoran
  • Petroutsos Dimitris
  Nature Communications, Nature Publishing Group, 2023, 14 (1), pp.2687. Abstract Availability of light and CO 2 , substrates of microalgae photosynthesis, is frequently far from optimal. Microalgae activate photoprotection under strong light, to prevent oxidative damage, and the CO 2 Concentrating Mechanism (CCM) under low CO 2 , to raise intracellular CO 2 levels. The two processes are interconnected; yet, the underlying transcriptional regulators remain largely unknown. Employing a large transcriptomic data compendium of Chlamydomonas reinhardtii’s responses to different light and carbon supply, we reconstruct a consensus genome-scale gene regulatory network from complementary inference approaches and use it to elucidate transcriptional regulators of photoprotection. We show that the CCM regulator LCR1 also controls photoprotection, and that QER7, a Squamosa Binding Protein, suppresses photoprotection- and CCM-gene expression under the control of the blue light photoreceptor Phototropin. By demonstrating the existence of regulatory hubs that channel light- and CO 2 -mediated signals into a common response, our study provides an accessible resource to dissect gene expression regulation in this microalga. (10.1038/s41467-023-38183-4)
  DOI : 10.1038/s41467-023-38183-4
• Scalable Generation of Pre‐Vascularized and Functional Human Beige Adipose Organoids
  
  • Escudero Mélanie
  • Vaysse Laurence
  • Eke Gozde
  • Peyrou Marion
  • Villarroya Francesc
  • Bonnel Sophie
  • Boyer Louisa
  • Vieu Christophe
  • Chaput Benoit
  • Yao Xi
  • Deschaseaux Frédéric
  • Parny Mélissa
  • Raymond-Letron Isabelle
  • Dani Christian
  • Carrière Audrey
  • Malaquin Laurent
  • Casteilla Louis
  Advanced Science, Wiley Open Access, 2023, 10 (31), pp.e2301499. Obesity and type 2 diabetes are becoming a global sociobiomedical burden. Beige adipocytes are emerging as key inducible actors and putative relevant therapeutic targets for improving metabolic health. However, in vitro models of human beige adipose tissue are currently lacking and hinder research into this cell type and biotherapy development. Unlike traditional bottom‐up engineering approaches that aim to generate building blocks, here a scalable system is proposed to generate pre‐vascularized and functional human beige adipose tissue organoids using the human stromal vascular fraction of white adipose tissue as a source of adipose and endothelial progenitors. This engineered method uses a defined biomechanical and chemical environment using tumor growth factor β (TGFβ) pathway inhibition and specific gelatin methacryloyl (GelMA) embedding parameters to promote the self‐organization of spheroids in GelMA hydrogel, facilitating beige adipogenesis and vascularization. The resulting vascularized organoids display key features of native beige adipose tissue including inducible Uncoupling Protein‐1 (UCP1) expression, increased uncoupled mitochondrial respiration, and batokines secretion. The controlled assembly of spheroids allows to translate organoid morphogenesis to a macroscopic scale, generating vascularized centimeter‐scale beige adipose micro‐tissues. This approach represents a significant advancement in developing in vitro human beige adipose tissue models and facilitates broad applications ranging from basic research to biotherapies. (10.1002/advs.202301499)
  DOI : 10.1002/advs.202301499
• Gas-particle partitioning of toluene oxidation products: an experimental and modeling study
  
  • Lannuque Victor
  • d'Anna Barbara
  • Kostenidou Evangelia
  • Couvidat Florian
  • Martinez-Valiente Alvaro
  • Eichler Philipp
  • Wisthaler Armin
  • Müller Markus
  • Temime-Roussel Brice
  • Valorso Richard
  • Sartelet Karine
  Atmospheric Chemistry and Physics Discussions, European Geosciences Union, 2023, 332, pp.121955. The higher concentrations of atmospheric particles, such as black carbon (BC) and organic matter (OM), detected in streets compared to the urban background are predominantly attributed to road traffic. The integration of this source of pollutant in air quality models nevertheless entails a high degree of uncertainty and some other sources may be missing. Through sensitivity scenarios, the impacts on pollutant concentrations of sensitivities related to traffic and road-asphalt emissions are evaluated. The 3D Eulerian model POLAIR3D and the street network model MUNICH are applied to simulate various scenarios and their impacts at the regional and local scales. They are coupled with the modular box model SSH-aerosol to represent formation and aging of primary and secondary gas and particles. Traffic emissions are calculated with the COPERT methodology. Using recent volatile organic compound speciations for light vehicles with more detailed information pertaining to intermediate, semi-and low-volatile organic compounds (I/S/LVOCs) leads to limited reductions of OM concentrations (10% in streets). Changing the method of estimating I/S/LVOC emissions leads to an average reduction of 60% at emission and a decrease of the OM concentrations of 27% at the local scale. An increase in 219% of BC emissions from tire wear, consistent with the uncertainties found in the literature, doubles the BC concentrations at the local scale, which remain underestimated compared to observations. I/S/LVOC emissions are several orders of magnitude higher when considering emissions from road asphalt due to pavement heating and exposure to sunlight. However, simulated concentrations of PM at the local scale remain within acceptable ranges compared to observations. These results suggest that more information is needed on I/S/LVOCs and non-exhaust sources (tire, brake and road abrasion) that impact the particle concentration. Furthermore, currently unconsidered emission sources such as road asphalt may have non-negligible impacts on pollutant concentrations in streets. ✩ This paper has been recommended for acceptance by Admir Créso Targino. (10.5194/egusphere-2023-1290)
  DOI : 10.5194/egusphere-2023-1290
• Chlorhexidine digluconate exerts bactericidal activity vs Gram positive Staphylococci with bioelectrocatalytic compatibility: High level disinfection for implantable biofuel cells
  
  • Berezovska Anastasiia
  • Meiller Anne
  • Marinesco Stéphane
  • Nedellec Yannig
  • Giroud Fabien
  • Gross Andrew J.
  • Cosnier Serge
  Bioelectrochemistry, Elsevier, 2023, 152, pp.108435. Implanted devices destined for contact with sterile body tissues, vasculature or fluids should be free of any microbial contamination that could lead to disease transmission. The disinfection and sterilisation of implantable biofuel cells is a challenging and largely overlooked subject due to the incompatibility of fragile biocatalytic components with classical treatments. Here we report the development of a convenient "soft" chemical treatment based on immersion of enzymatic bioelectrodes and biofuel cells in dilute aqueous chlorhexidine digluconate (CHx). We show that immersion treatment in a 0.5 % solution of CHx for 5 min is sufficient to remove 10-6 log colony forming units of Staphylococcus hominis after 26 h while shorter treatments are less effective. Treatments with 0.2 % CHx solutions were ineffective. Bioelectrocatalytic half-cell voltammetry revealed no loss in activity at the bioanode after the bactericidal treatment, while the cathode was less tolerant. A maximum power output loss of ca. 10 % for the glucose/O2 biofuel cell was observed following the 5 min CHx treatment, while the dialysis bag had a significant negative impact on the power output. Finally, we report a proof-of-concept in vivo operation for 4 days of a CHx-treated biofuel cell with a 3D printed holder and additional porous surgical tissue interface. Further assessments are necessary to rigorously validate sterilisation, biocompatibility and tissue response performance. (10.1016/j.bioelechem.2023.108435)
  DOI : 10.1016/j.bioelechem.2023.108435
• Wind power predictions from nowcasts to 4-hour forecasts: a learning approach with variable selection
  
  • Bouche Dimitri
  • Flamary Rémi
  • D’alché-Buc Florence
  • Plougonven Riwal
  • Clausel Marianne
  • Badosa Jordi
  • Drobinski Philippe
  Renewable Energy, Elsevier, 2023, 211, pp.938-947. We study short-term prediction of wind speed and wind power (every 10 minutes up to 4 hours ahead). Accurate forecasts for these quantities are crucial to mitigate the negative effects of wind farms' intermittent production on energy systems and markets. We use machine learning to combine outputs from numerical weather prediction models with local observations. The former provide valuable information on higher scales dynamics while the latter gives the model fresher and location-specific data. So as to make the results usable for practitioners, we focus on well-known methods which can handle a high volume of data. We study first variable selection using both a linear technique and a nonlinear one. Then we exploit these results to forecast wind speed and wind power still with an emphasis on linear models versus nonlinear ones. For the wind power prediction, we also compare the indirect approach (wind speed predictions passed through a power curve) and the indirect one (directly predict wind power). (10.1016/j.renene.2023.05.005)
  DOI : 10.1016/j.renene.2023.05.005
• Paléoenvironnements et sociétés humaines. Projets financés sur la période 2005-2022
  
  • Ghilardi Matthieu
  • Pateau Mélanie
  Les Cahiers de l'ANR, Paris : ANR Agence nationale de la recherche, 2009-, 2023. Le présent cahier a pour thème principal les interactions entre les sociétés humaines du passé et les milieux dans lesquels elles ont évolué. Il fait référence aux différents projets de recherche financés par l’ANR dans ce domaine. Ce cahier, le 15e de la collection, a été conçu par Matthieu Ghilardi, président de comité d’évaluation scientifique, et Mélanie Pateau, chargée de projets scientifiques, en collaboration avec la Direction de l’information et de la communication. Ce document est une première version. Pour voir les différentes mises à jour du document, rendez-vous sur : https://anr.fr/fr/ressources/cahiers-thematiques
• A middleware architecture for mastering energy consumption in internet of things applications
  
  • Borges Caldas da Silva Pedro Victor
  • Taconet Chantal
  • Chabridon Sophie
  • Conan Denis
  • Cavalcante Everton
  , 2023. The Internet of things (IoT) has been identified as a significant contributor to increasing Information and Communication Technology (ICT) energy consumption in the future. Carefully designing interactions between client applications and systems in the IoT may positively impact energy saving. For this purpose, IoT middleware, the underlying software that manages those interactions, should consider energy efficiency strategies a first-class concern. Furthermore, adding an energy-awareness capability to the middleware could significantly contribute to deepening developers' understanding of energy consumption by applications and helping them minimize the energy demand. In this paper, we propose energy-efficiency strategies and integrate them into an IoT middleware. We also offer a model to calculate the energy consumption of the interactions between an IoT consumer application and an IoT system, which the middleware could use to choose the best strategy to constrain the application's energy consumption to a given budget. (10.1109/ICT4S58814.2023.00016)
  DOI : 10.1109/ICT4S58814.2023.00016
• The basolateral amygdala-anterior cingulate pathway contributes to depression-like behaviors and comorbidity with chronic pain behaviors in male mice
  
  • Becker Léa J.
  • Fillinger Clementine
  • Waegaert Robin
  • Journée Sarah
  • Hener Pierre
  • Ayazgök Beyza
  • Humo Muris
  • Karatas Meltem
  • Thouaye Maxime
  • Gaikwad Mithil
  • Degiorgis Laetitia
  • Santin Marie Des Neiges
  • Mondino Mary
  • Barrot Michel
  • Ibrahim El Chérif
  • Turecki Gustavo
  • Belzeaux Raoul
  • Veinante Pierre
  • Harsan Laura
  • Hugel Sylvain
  • Lutz Pierre-Eric
  • Yalcin Ipek
  Nature Communications, Nature Publishing Group, 2023, 14 (1). While depression and chronic pain are frequently comorbid, underlying neuronal circuits and their psychopathological relevance remain poorly defined. Here we show in mice that hyperactivity of the neuronal pathway linking the basolateral amygdala to the anterior cingulate cortex is essential for chronic pain-induced depression. Moreover, activation of this pathway in naive male mice, in the absence of on-going pain, is sufficient to trigger depressive-like behaviors, as well as transcriptomic alterations that recapitulate core molecular features of depression in the human brain. These alterations notably impact gene modules related to myelination and the oligodendrocyte lineage. Among these, we show that Sema4a, which was significantly upregulated in both male mice and humans in the context of altered mood, is necessary for the emergence of emotional dysfunction. Overall, these results place the amygdalo-cingulate pathway at the core of pain and depression comorbidity, and unravel the role of Sema4a and impaired myelination in mood control. (10.1038/s41467-023-37878-y)
  DOI : 10.1038/s41467-023-37878-y
• Statistical Downscaling to Improve the Subseasonal Predictions of Energy-Relevant Surface Variables
  
  • Goutham Naveen
  • Plougonven Riwal
  • Omrani Hiba
  • Tantet Alexis
  • Parey Sylvie
  • Tankov Peter
  • Hitchcock Peter
  • Drobinski Philippe
  Monthly Weather Review, American Meteorological Society, 2023, 151, pp.275-296. Owing to the increasing share of variable renewable energies in the electricity mix, the European energy sector is becoming more weather sensitive. In this regard, skillful subseasonal predictions of essential climate variables can provide considerable socioeconomic benefits to the energy sector. The aim of this study is therefore to improve the European subseasonal predictions of 100-m wind speed and 2-m temperature, which we achieve through statistical downscaling. We employ redundancy analysis (RDA) to estimate spatial patterns of variability from large-scale fields that allow for the best prediction of surface fields. We compare explanatory powers between the patterns obtained using RDA against those derived using principal component analysis (PCA), when used as predictors in multilinear regression models to predict surface fields, and show that the explanatory power of the former is superior to that of the latter. Subsequently, we employ the estimated relationship between RDA patterns and surface fields to produce statistical probabilistic predictions of gridded surface fields using dynamical ensemble predictions of RDA patterns. We finally demonstrate how a simple combination of dynamical and statistical predictions of surface fields significantly improves the accuracy of subseasonal predictions of both variables over a large part of Europe. We attribute the improved accuracy of these combined predictions to improvements in reliability and resolution. (10.1175/MWR-D-22-0170.1)
  DOI : 10.1175/MWR-D-22-0170.1
• Janus effect of the anterior cingulate cortex: Pain and emotion
  
  • Journée Sarah H
  • Mathis Victor P
  • Fillinger Clémentine
  • Veinante Pierre
  • Yalcin Ipek
  Neuroscience and Biobehavioral Reviews, Elsevier, 2023, 153, pp.105362. Over the past 20 years, clinical and preclinical studies point to the anterior cingulate cortex (ACC) as a site of interest for several neurological and psychiatric conditions. The ACC plays a critical role in emotion, autonomic regulation, pain processing, attention, memory and decision making. An increasing number of studies have demonstrated the involvement of the ACC in the emotional component of pain and its comorbidity with emotional disorders such as anxiety and depression. Thanks to the development of animal models combined with state-of-the-art technologies, we now have a better mechanistic understanding of the functions of the ACC. Hence, the primary aim of this review is to compile the most recent preclinical studies on the role of ACC in the emotional component and consequences of chronic pain. Herein, we thus thoroughly describe the pain-induced electrophysiological, molecular and anatomical alterations in the ACC and in its related circuits. Finally, we discuss the next steps that are needed to strengthen our understanding of the involvement of the ACC in emotional and pain processing. (10.1016/j.neubiorev.2023.105362)
  DOI : 10.1016/j.neubiorev.2023.105362
• Nucleosome patterns in four plant pathogenic fungi with contrasted genome structures
  
  • Clairet Colin
  • Lapalu Nicolas
  • Simon Adeline
  • Soyer Jessica
  • Viaud Muriel
  • Zehraoui Enric
  • Dalmais Berengère
  • Fudal Isabelle
  • Ponts Nadia
  Peer Community Journal, Peer Community In, 2023, 3, pp.e13. Fungal pathogens represent a serious threat towards agriculture, health, and environment. Control of fungal diseases on crops necessitates a global understanding of fungal pathogenicity determinants and their expression during infection. Genomes of phytopathogenic fungi are often compartmentalized: the core genome contains housekeeping genes whereas the fast-evolving genome mainly contains transposable elements and species-specific genes. In this study, we analysed nucleosome landscapes of four phytopathogenic fungi with contrasted genome organizations to describe and compare nucleosome repartition patterns in relation with genome structure and gene expression level. We combined MNase-seq and RNA-seq analyses to concomitantly map nucleosome-rich and transcriptionally active regions during fungal growth in axenic culture; we developed the MNase-seq Tool Suite (MSTS) to analyse and visualise data obtained from MNase-seq experiments in combination with other genomic data and notably RNA-seq expression data. We observed different characteristics of nucleosome profiles between species, as well as between genomic regions within the same species. We further linked nucleosome repartition and gene expression. Our findings support that nucleosome positioning and occupancies are subjected to evolution, in relation with underlying genome sequence modifications. Understanding genomic organization and its role in expression regulation is the next gear to understand complex cellular mechanisms and their evolution. (10.24072/pcjournal.227)
  DOI : 10.24072/pcjournal.227
• Unsymmetrical boron diketonates containing strong electron-donating groups as mechanochromic fluorescent solids
  
  • Mehiaoui Nawel
  • Leleu Stéphane
  • Kibou Zahira
  • Choukchou-Braham Noureddine
  • Franck Xavier
  • Gallavardin Thibault
  Dyes and Pigments, Elsevier, 2023, 208, pp.110829. New π-conjugated unsymmetrical β-diketones were synthesized thanks to a modular synthetic approach involving in situ generated acylketenes through thermal degradation of 1,4-dioxin-2-ones. This method gave access to a family of new chromophores featuring either an indoline or a benzothiazole as electron-donating groups in one side and various aromatic moieties in the other side. After complexation with boron difluoride, BDK (Boron DiKetonates) compounds were obtained featuring fluorescence in non-polar solvents. These compounds were also found to be fluorescent in solid state with quantum yield up to 0.22, and their emission wavelength was very sensitive to their crystallinity. Two of these compounds were successfully recrystallized to provide small single crystals and emission spectra were recorded in crystal phase and ground state which showed mechanochromism with a spectral shift of 37 nm. (10.1016/j.dyepig.2022.110829)
  DOI : 10.1016/j.dyepig.2022.110829