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1. Fast and Bioorthogonal Release of Isocyanates in Living Cells from Iminosydnones and Cycloalkynes

Author: Maxime Ribéraud, Karine Porte, Arnaud Chevalier, Léa Madegard, Aurélie Rachet, Agnès Delaunay-Moisan, Florian Vinchon, Pierre Thuéry, Giovanni Chiappetta, Pier Alexandre Champagne, Grégory Pieters, Davide Audisio, Frédéric Taran, CEA- Saclay (CEA), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Service de Chimie Bio-Organique et de Marquage (SCBM), Médicaments et Technologies pour la Santé (MTS), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de Chimie des Substances Naturelles (ICSN), Institut de Chimie du CNRS (INC)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Nanosciences et Innovation pour les Matériaux, la Biomédecine et l'Energie (ex SIS2M) (NIMBE UMR 3685), Institut Rayonnement Matière de Saclay (IRAMIS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL), New Jersey Institute of Technology [Newark] (NJIT), ANR-11-EQPX-0029,MORPHOSCOPE 2,Imagerie et reconstruction multiéchelles de la morphogenèse. (Plateforme d'innovation technologique et méthodologique pour l'imagerie in vivo et la reconstruction des dynamiques multiéchelles de la morphogenèse)(2011), ANR-10-INBS-0004,France-BioImaging,Développment d'une infrastructure française distribuée coordonnée(2010), ANR-11-IDEX-0003,IPS,Idex Paris-Saclay(2011), and ANR-19-CE06-0006,NanoClick,Micelles clivables par chimie bioorthogonale(2019)
Subjects: Colloid and Surface Chemistry, [SDV]Life Sciences [q-bio], General Chemistry, Biochemistry, Catalysis
Abstract: International audience; Bioorthogonal click and release reactions are powerful tools for chemical biology allowing, for example, the selective release of drugs in biological media, including inside animals. Here we developed two new families of iminosydnone mesoionic reactants that allow a bioorthogonal release of electrophilic species under physiological conditions. Their synthesis and reactivities as dipoles in cycloaddition reactions with strained alkynes have been studied in detail. Whereas the impact of the pH on the reaction kinetics was demonstrated experimentally, theoretical calculations suggest that the newly designed dipoles display reduced resonance stabilization energies compared to previously described iminosydnones explaining their higher reactivity. These mesoionic compounds react smoothly with cycloalkynes under physiological, copper-free reaction conditions to form a click pyrazole product together with a released alkyl-or aryl-isocyanate. With kinetic constants up to 1000 M-1 s-1 , this click and release reaction is among the fastest described to date, and represents the first bioorthogonal process allowing the release of isocyanate electrophiles inside living cells offering interesting perspectives in chemical biology.
Published: 2023

2. Harmonic Disturbance Compensation of a System With Long Dead-Time, Design and Experimental Validation

Author: Can Kutlu Yüksel, Tomáš Vyhlídal, Jaroslav Bušek, Milan Anderle, Silviu-Iulian Niculescu, Laboratoire des signaux et systèmes (L2S), CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Czech Technical University in Prague (CTU), Faculty of Mechanical Engineering [Prague] (CTU/FME), Institute of Information Theory and Automation of the Czech Academy of Sciences (UTIA / CAS), Czech Academy of Sciences [Prague] (CAS), Dynamical Interconnected Systems in COmplex Environments (DISCO), Inria Saclay - Ile de France, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire des signaux et systèmes (L2S), CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Agency of the Czech Technical University in Prague under Grant SGS23/157/OHK2/3T/12., and ANR-11-IDEX-0003,IPS,Idex Paris-Saclay(2011)
Subjects: internal model, Periodic disturbance, Control and Systems Engineering, frequency methods, Electrical and Electronic Engineering, time delay, [SPI.AUTO]Engineering Sciences [physics]/Automatic, Computer Science Applications
Abstract: International audience; An internal model control scheme is proposed to compensate both a long dead-time of a system and a harmonic disturbance. The controller is based on an inversion of the firstorder model used to approximate the system dynamics together with an input delay. Two other components of the controller consist of a filter and an additional delay by which the harmonic modes are targeted via adjusting the control loop gain and phase shift. The design of the filter-delay pair is fully analytical and the implementation of the scheme is straightforward. The main attention is paid to the complete compensation of a single harmonic disturbance. Besides, an extension of the scheme is proposed to target a double harmonic disturbance. Increased attention is paid to the robustness aspects of the schemes. Outstanding performance in terms of harmonic disturbance compensation of the proposed schemes is demonstrated on a series of laboratory experiments.
Published: 2023

3. A simple and efficient process for the synthesis of 2D carbon nitrides and related materials

Author: Huc, Vincent, Silva, Cora, Vallet, Maxime, Saint-Martin, Romuald, Leroy, Jocelyne, Semion, Clément, Dragoe, Diana, Brisset, François, Blin, Thomas, Guillot, Regis, Gillet, Cynthia, Université Paris-Saclay, ONERA, CNRS, Laboratoire d'étude des microstructures (LEM), ONERA-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Mécanique Paris-Saclay (LMPS), CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Ecole Normale Supérieure Paris-Saclay (ENS Paris Saclay), Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), Institut de Chimie du CNRS (INC)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Nanosciences et Innovation pour les Matériaux, la Biomédecine et l'Energie (ex SIS2M) (NIMBE UMR 3685), Institut Rayonnement Matière de Saclay (IRAMIS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), ANR-11-EQPX-0029,MORPHOSCOPE 2,Imagerie et reconstruction multiéchelles de la morphogenèse. (Plateforme d'innovation technologique et méthodologique pour l'imagerie in vivo et la reconstruction des dynamiques multiéchelles de la morphogenèse)(2011), ANR-10-INBS-0004,France-BioImaging,Développment d'une infrastructure française distribuée coordonnée(2010), ANR-11-IDEX-0003,IPS,Idex Paris-Saclay(2011), CentraleSupélec, Laboratoire Innovation en Chimie des Surfaces et NanoSciences (LICSEN UMR 3685), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut Rayonnement Matière de Saclay (IRAMIS), and ANR-10-LABX-0040,SPS,Saclay Plant Sciences(2010)
Subjects: [CHIM.MATE]Chemical Sciences/Material chemistry
Abstract: This manuscript describes a new process for the synthesis of very high quality 2D Covalent Organic Frameworks (COFs), such a C2N and CN carbon nitrides. The structure/quality of these materials is demonstrated by extensive cross-characterisations at different scales. The availability of such very large, high quality layers of these materials opens interesting perspectives, for example in photochemistry and electronics (intrinsic transport properties, high gap substrate for graphene, etc...). We thus consider that this work could be of interest to a broad readership, considering that this topic is among the current hottest ones.
Published: 2023

4. A Spectrum-based Filter Design for Periodic Output Regulation of Systems with Dead-Time

Author: Yuksel, Can Kutlu, Vyhlídal, Tomáš, Niculescu, Silviu-Iulian, Laboratoire des signaux et systèmes (L2S), CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Czech Technical University in Prague (CTU), Dynamical Interconnected Systems in COmplex Environments (DISCO), Inria Saclay - Ile de France, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire des signaux et systèmes (L2S), CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Student Grant Agency of the Czech Technical University in Prague, student grant No. SGS23/157/OHK2/3T/12., and ANR-11-IDEX-0003,IPS,Idex Paris-Saclay(2011)
Subjects: IMC, delay, filter design, vibration control, delay filter design IMC vibration control, [SPI.AUTO]Engineering Sciences [physics]/Automatic
Abstract: International audience; This paper presents a filter structure that allows the user to place desired poles and the necessary zeros to achieve periodic regulation to the closed-loop sensitivity through Internal Model Control framework. The periodic regulation is aimed at stable SISO linear systems suffering from input dead-time and having no closed right-half plane zeros. The negative effects of the dead time on tracking/rejection are compensated by introducing another delay which is tuned independently from the filter thanks to its structure. The main focus is given to constructing the filter with polynomials. However, it can be readily extended to quasi-polynomials. The findings are verified with a computer simulation of a vibration control task.
Published: 2023

5. In Vivo Fast Nonlinear Microscopy Reveals Impairment of Fast Axonal Transport Induced by Molecular Motor Imbalances in the Brain of Zebrafish Larvae

Author: Baptiste Grimaud, Maxence Frétaud, Feriel Terras, Antoine Bénassy, Karine Duroure, Valérie Bercier, Gaëlle Trippé-Allard, Rabei Mohammedi, Thierry Gacoin, Filippo Del Bene, François Marquier, Christelle Langevin, François Treussart, Treussart, François, APPEL À PROJETS TRANSNATIONAL SUR LA NANOMÉDECINE - - MoDiaNo2018 - ANR-18-ENM3-0002 - ERAnet EURONANOMED - VALID, Enabling Vision Restoration - - FOReSIGHT2018 - ANR-18-IAHU-0001 - IAHU - VALID, Comprendre comment l'homéostasie du transport axonal est médiée par le 'tubulin code' - - CodeAx2020 - ANR-20-CE13-0011 - AAPG2020 - VALID, iReelAx : Analyse interspécifique des fonctions de Reelin dans le câblage des circuits et les troubles neurodéveloppementaux - - iReelAx2019 - ANR-19-CE16-0017 - AAPG2019 - VALID, Idex Paris-Saclay - - IPS2011 - ANR-11-IDEX-0003 - IDEX - VALID, Laboratoire Lumière, Matière et Interfaces (LuMIn), CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Ecole Normale Supérieure Paris-Saclay (ENS Paris Saclay), Plateforme d'Infectiologie Expérimentale des Rongeurs et Poissons (IERP (UE 0907)), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Virologie et Immunologie Moléculaires (VIM (UR 0892)), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de la Vision, Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), VIB Center for Brain and Disease Research, Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Laboratoire de physique de la matière condensée (LPMC), École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS), MITI CNRS- Fondation pour la recherche médicale (grant #MND202003011485)- FWO Fellowship (#12Y9120N), ANR-18-ENM3-0002,MoDiaNo(2018), ANR-18-IAHU-0001,FOReSIGHT,Enabling Vision Restoration(2018), ANR-20-CE13-0011,CodeAx,Comprendre comment l'homéostasie du transport axonal est médiée par le 'tubulin code'(2020), ANR-19-CE16-0017,iReelAx,iReelAx : Analyse interspécifique des fonctions de Reelin dans le câblage des circuits et les troubles neurodéveloppementaux(2019), and ANR-11-IDEX-0003,IPS,Idex Paris-Saclay(2011)
Subjects: [PHYS.PHYS.PHYS-OPTICS] Physics [physics]/Physics [physics]/Optics [physics.optics], [PHYS.PHYS.PHYS-OPTICS]Physics [physics]/Physics [physics]/Optics [physics.optics], second harmonic generation, [SDV.IB.IMA]Life Sciences [q-bio]/Bioengineering/Imaging, General Engineering, General Physics and Astronomy, nonlinear nanocrystal, disease models, molecular motor, [SDV.IB.IMA] Life Sciences [q-bio]/Bioengineering/Imaging, zebrafish larva, [SDV.NEU]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC], General Materials Science, two-photon microscopy, [SDV.NEU] Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC], axonal transport, single nanoparticle tracking
Abstract: International audience; Cargo transport by molecular motors along microtubules is essential for the function of eucaryotic cells, in particular neurons in which axonal transport defects constitute the early pathological features of neurodegenerative diseases. Mainly studied in motor and sensory neurons, axonal transport is still difficult to characterize in neurons of the brain in absence of appropriate in vivo tools. Here, we measured fast axonal transport by tracing the second harmonic generation (SHG) signal of potassium titanyl phosphate (KTP) nanocrystals endocytosed by brain neurons of zebrafish (Zf) larvae. Thanks to the optical translucency of Zf larvae and of the perfect photostability of nanoKTP SHG, we achieved a high scanning speed of 20 frames (of ≈ 90 μ m×60 μ m size) per second in Zf brain. We focused our study on endolysosomal vesicle transport in axons of known polarization, separately analyzing kinesin and dynein motor-driven displacements. To validate our assay, we used either loss-of-function mutations of dynein or kinesin 1 or the dynein inhibitor dynapyrazole, and quantified several transport parameters. We successfully demonstrated that dynapyrazole reduces nanoKTP mobile fraction and retrograde run length consistently, while the retrograde run length increased in kinesin 1 mutants. Taking advantage of nanoKTP SHG directional emission, we also quantified fluctuations of vesicle orientation. Thus, by combining endocytosis of nanocrystals having non-linear response, fast two-photon microscopy, and high-throughput analysis, we are able to finely monitor fast axonal transport in vivo in the brain of a vertebrate, and reveal subtle axonal transport alterations. The high spatiotemporal resolution achieved in our model may be relevant to precisely investigate axonal transport impairment associated to disease models.
Published: 2022

6. Adenylates regulate Arabidopsis plastidial thioredoxin activities through the binding of a CBS domain protein

Author: Kevin Baudry, Félix Barbut, Séverine Domenichini, Damien Guillaumot, Mai Pham Thy, Hélène Vanacker, Wojciech Majeran, Anja Krieger-Liszkay, Emmanuelle Issakidis-Bourguet, Claire Lurin, Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), ANR-17-EURE-0003,CBH-EUR-GS,CBH-EUR-GS(2017), ANR-11-IDEX-0003,IPS,Idex Paris-Saclay(2011), and ANR-10-INBS-0005,FRISBI,Infrastructure Française pour la Biologie Structurale Intégrée(2010)
Subjects: Chloroplasts, Arabidopsis Proteins, Physiology, [SDV]Life Sciences [q-bio], Arabidopsis, Cystathionine beta-Synthase, Plant Science, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, Adenosine Monophosphate, Chloroplast Proteins, Adenosine Triphosphate, Thioredoxins, Genetics, Plastids, Sulfhydryl Compounds, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], Oxidation-Reduction, Research Articles
Abstract: Cystathionine-β-synthase (CBS) domains are found in proteins of all living organisms and have been proposed to play a role as energy sensors regulating protein activities through their adenosyl ligand binding capacity. In plants, members of the CBSX protein family carry a stand-alone pair of CBS domains. In Arabidopsis (Arabidopsis thaliana), CBSX1 and CBSX2 are targeted to plastids where they have been proposed to regulate thioredoxins (TRXs). TRXs are ubiquitous cysteine thiol oxido-reductases involved in the redox-based regulation of numerous enzymatic activities as well as in the regeneration of thiol-dependent peroxidases. In Arabidopsis, 10 TRX isoforms have been identified in plastids and divided into five sub-types. Here, we show that CBSX2 specifically inhibits the activities of m-type TRXs toward two chloroplast TRX-related targets. By testing activation of NADP-malate dehydrogenase and reduction of 2-Cys peroxiredoxin, we found that TRXm1/2 inhibition by CBSX2 was alleviated in the presence of AMP or ATP. We also determined, by pull-down assays, a direct interaction of CBSX2 with reduced TRXm1 and m2 that was abolished in the presence of adenosyl ligands. In addition, we report that, compared with wild-type plants, the Arabidopsis T-DNA double mutant cbsx1 cbsx2 exhibits growth and chlorophyll accumulation defects in cold conditions, suggesting a function of plastidial CBSX proteins in plant stress adaptation. Together, our results show an energy-sensing regulation of plastid TRX m activities by CBSX, possibly allowing a feedback regulation of ATP homeostasis via activation of cyclic electron flow in the chloroplast, to maintain a high energy level for optimal growth.
Published: 2022

7. Neutron and beta imaging with Micromegas detectors with optical readout

Author: A. Cools, S. Aune, F. Beau, M. Benali, F.M. Brunbauer, T. Benoit, D. Desforge, E. Ferrer-Ribas, C. Malgorn, E. Oliveri, T. Papaevangelou, E.C. Pollacco, L. Ropelewski, A. Sari, Institut de Recherches sur les lois Fondamentales de l'Univers (IRFU), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Institut des Sciences du Vivant Frédéric JOLIOT (JOLIOT), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Laboratoire Capteurs et Architectures Electroniques (LCAE), Département Métrologie Instrumentation & Information (DM2I), Laboratoire d'Intégration des Systèmes et des Technologies (LIST (CEA)), Direction de Recherche Technologique (CEA) (DRT (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Technologique (CEA) (DRT (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Laboratoire d'Intégration des Systèmes et des Technologies (LIST (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, CERN [Genève], ANR-10-LABX-0038,P2IO,Physics of the 2 infinities and the origins(2010), and ANR-11-IDEX-0003,IPS,Idex Paris-Saclay(2011)
Subjects: instrumentation, Nuclear and High Energy Physics, Neutron-gamma discrimination, Beta imager, detector, Gamma imaging, neutrons, gamma-rays, Glass Micromegas, X-rays, beta-rays, Neutron radiography, Gaseous detector, [PHYS.PHYS.PHYS-INS-DET]Physics [physics]/Physics [physics]/Instrumentation and Detectors [physics.ins-det], Micromegas, nuclear instrumentation, Optical readout, MPGD
Abstract: International audience; Recent developments have shown that coupling a Micromegas gaseous detector on a glass substrate with a transparent anode and a CMOS camera enables the optical readout of Micromegas detectors with a good spatial resolution, demonstrating that the glass Micromegas detector is well-suited for imaging. This feasibility test has been effectuated with low-energy X-ray photons also permitting energy resolved imaging. This test opens the way to different applications. Here we will focus on two applications. Namely, neutron imaging for non-destructive examination of highly gamma-ray emitting objects, such as irradiated nuclear fuel or radioactive waste. And secondly, we are developing a beta imager for the cell tagging in the field of anticancerous drug studies.Both applications require to design the detectors in view of the specific constraints of reactor dismantling and medical applications: spatial resolution and strong gamma suppression for neutron imaging and precise rate and energy spectrum measurements for the beta.A dedicated system consisting of a glass Micromegas detector and an ultrasensitive camera has been designed and assembled. Here we present the first results from the characterization of the detectors, as well as the first acquired images.
Published: 2023

8. Invisible dilaton

Author: Philippe Brax, Clare Burrage, Jose A. R. Cembranos, Patrick Valageas, Institut de Physique Théorique - UMR CNRS 3681 (IPHT), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), University of Nottingham, UK (UON), IPARCOS Institute and EMFTEL Department, Universidad Complutense de Madrid, Universidad Complutense de Madrid = Complutense University of Madrid [Madrid] (UCM), ANR-11-IDEX-0003,IPS,Idex Paris-Saclay(2011), and ANR-10-LABX-0038,P2IO,Physics of the 2 infinities and the origins(2010)
Subjects: scalar, Astrophysics and Astronomy, potential, gr-qc, satellite, halo, field theory, symmetry breaking, dark matter, thermal, local, radiative correction, Particle Physics - Phenomenology, electroweak interaction, General Relativity and Cosmology, fluctuation, background, screening, effective potential, hep-ph, alignment, oscillation, stability, condensation, scalar particle, equivalence principle, gravitation, [PHYS.HPHE]Physics [physics]/High Energy Physics - Phenomenology [hep-ph], astro-ph.CO, [PHYS.GRQC]Physics [physics]/General Relativity and Quantum Cosmology [gr-qc], mass, violation, [PHYS.ASTR]Physics [physics]/Astrophysics [astro-ph], dilaton, Higgs, symmetron
Abstract: We analyze the dynamics of a light scalar field responsible for the μ term of the Higgs potential and coupled to matter via the Higgs-portal mechanism. We find that this dilaton model is stable under radiative corrections induced by the standard model particle masses. When the background value of the scalar field is stabilized at the minimum of the scalar potential, the scalar field fluctuations only couple quadratically to the massive fields of the standard model preventing the scalar direct decay into standard model particles. Cosmologically and prior to the electroweak symmetry breaking, the scalar field rolls down along its effective potential before eventually oscillating and settling down at the electroweak minimum. These oscillations can be at the origin of dark matter due to the initial misalignment of the scalar field compared to the electroweak minimum, and we find that, when the mass of the scalar field is less than the electron volt scale and acts as a condensate behaving like dark matter on large scales, the scalar particles cannot thermalize with the standard model thermal bath. As matter couples in a composition-dependent manner to the oscillating scalar, this could lead to a violation of the equivalence principle aboard satellites such as the MICROSCOPE experiment and the next generation of tests of the equivalence principle. Local gravitational tests are evaded thanks to the weakness of the quadratic coupling in the dark matter halo, and we find that, around other sources, these dilaton models could be subject to a screening akin to the symmetron mechanism. We analyse the dynamics of a light scalar field responsible for the $\mu$ term of the Higgs potential and coupled to matter via the Higgs-portal mechanism. We find that this dilaton model is stable under radiative corrections induced by the standard model particle masses. When the background value of the scalar field is stabilised at the minimum of the scalar potential, the scalar field fluctuations only couple quadratically to the massive fields of the standard model preventing the scalar direct decay into standard model particles. Cosmologically and prior to the electroweak symmetry breaking, the scalar field rolls down along its effective potential before eventually oscillating and settling down at the electroweak minimum. These oscillations can be at the origin of dark matter due to the initial misalignment of the scalar field compared to the electroweak minimum, and we find that, when the mass of the scalar field is less than the eV scale and acts as a condensate behaving like dark matter on large scales, the scalar particles cannot thermalise with the standard model thermal bath. As matter couples in a composition-dependent manner to the oscillating scalar, this could lead to a violation of the equivalence principle aboard satellites such as the MICROSCOPE experiment and the next generation of tests of the equivalence principle. Local gravitational tests are evaded thanks to the weakness of the quadratic coupling in the dark matter halo, and we find that, around other sources, these dilaton models could be subject to a screening akin to the symmetron mechanism.
Published: 2023

9. Modeling compartmentalization within intracellular signaling pathway

Author: Alamichel, Claire, Calvo, Juan, Hingant, Erwan, Latrach, Saoussen, Quiblier, Nathan, Yvinec, Romain, Laboratoire de Mathématiques et Modélisation d'Evry (LaMME), Université d'Évry-Val-d'Essonne (UEVE)-ENSIIE-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Universidad de Granada = University of Granada (UGR), Laboratoire Amiénois de Mathématique Fondamentale et Appliquée - UMR CNRS 7352 (LAMFA), Université de Picardie Jules Verne (UPJV)-Centre National de la Recherche Scientifique (CNRS), Université Sorbonne Paris Nord, La pharmacologie des neurones et des astrocytes à l’aide des sciences du numérique (AISTROSIGHT), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre Hospitalier Lyon Sud [CHU - HCL] (CHLS), Hospices Civils de Lyon (HCL)-Hospices Civils de Lyon (HCL)- Theranexus [Lyon]-Inria Lyon, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Physiologie de la reproduction et des comportements [Nouzilly] (PRC), Institut Français du Cheval et de l'Equitation [Saumur] (IFCE)-Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Dynamiques de populations multi-échelles pour des systèmes physiologiques (MUSCA), Inria Saclay - Ile de France, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Physiologie de la reproduction et des comportements [Nouzilly] (PRC), Institut Français du Cheval et de l'Equitation [Saumur] (IFCE)-Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Français du Cheval et de l'Equitation [Saumur] (IFCE)-Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Mathématiques et Informatique Appliquées du Génome à l'Environnement [Jouy-En-Josas] (MaIAGE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and ANR-11-IDEX-0003,IPS,Idex Paris-Saclay(2011)
Subjects: Mathematics - Analysis of PDEs, FOS: Mathematics, [MATH.MATH-AP]Mathematics [math]/Analysis of PDEs [math.AP], [SDV.BBM.MN]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular Networks [q-bio.MN], Analysis of PDEs (math.AP)
Abstract: We present a new modeling approach for G protein coupled receptors signaling systems, that take into account the compartmentalization of receptors and their effectors, both at plasma membrane and in dynamic intra-cellular vesicles called endosomes. The first building block of the model is about compartment dynamics. It takes into account creation of de-novo endosomes, i.e. endocytosis, recycling of endosomes back to plasma membrane, degradation through transfer into lysosomes as well as endosomes fusion through coagulation dynamics. The second building block is biochemical reactions into each compartments and the transfer of molecules between the dynamical compartments. In this work, we prove sufficient conditions to obtain exponentially ergodicity for the size distribution of intracellular compartments. We futher design a finite volume scheme to simulate our model and show two application cases for receptor trafficking and spatially biased second effector signaling.
Published: 2023
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10. Thermal Shear Waves Induced in Mesoscopic Liquids at Low Frequency Mechanical Deformation

Author: Kume, Eni, Noirez, Laurence, LLB - Nouvelles frontières dans les matériaux quantiques (NFMQ), Laboratoire Léon Brillouin (LLB - UMR 12), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), ANR-11-IDEX-0003,IPS,Idex Paris-Saclay(2011), and European Project: 766007,MAMI
Subjects: Condensed Matter::Soft Condensed Matter, [PHYS]Physics [physics], Physics::Fluid Dynamics, Soft Condensed Matter (cond-mat.soft), FOS: Physical sciences, General Physics and Astronomy, General Chemistry, Condensed Matter - Soft Condensed Matter
Abstract: We show that a viscous liquid confined between two low thermal conductive surfaces (Al2O3) emit a thermal response upon applying a low frequency (Hz) shear excitation. Hot and cold thermal waves are observed in situ at atmospheric pressure and room temperature, in polypropylene glycol layers of various thicknesses ranging from 100 microns up to 340 microns, upon applying a mechanical oscillatory shear strain. The observed thermal effects, synchronous with the mechanical excitation, are inconsistent with a homogeneous viscous flow. It indicates that mesoscopic liquids are able to (partly) convert mechanical shear energy in non-equilibrium thermodynamic states. This effect called thermoelasticity is well known in solid materials. The observation of a thermal coupling to the mechanical shear deformation reinforces the assumption of elastically correlated liquid molecules. The amplitude of the thermoelastic waves increases linearly by increasing the shear strain amplitude up to a transition to a non-linear thermal behavior, similar in strain behavior to an elastic to plastic regime. The thermo-elastic effects are not detectable via stress measurements and thus appear as a complementary liquid dynamic characterization., Comment: 10_pages
Published: 2022

11. Interactive Information Design

Author: Frédéric Koessler, Marie Laclau, Tristan Tomala, Paris School of Economics (PSE), École des Ponts ParisTech (ENPC)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Paris 1 Panthéon-Sorbonne (UP1)-Centre National de la Recherche Scientifique (CNRS)-École des hautes études en sciences sociales (EHESS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Paris Jourdan Sciences Economiques (PJSE), Université Paris 1 Panthéon-Sorbonne (UP1)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École des hautes études en sciences sociales (EHESS)-École des Ponts ParisTech (ENPC)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Groupement de Recherche et d'Etudes en Gestion (GREGHEC ), Ecole des Hautes Etudes Commerciales (HEC Paris)-Centre National de la Recherche Scientifique (CNRS), Ecole des Hautes Etudes Commerciales (HEC Paris), ANR-17-EURE-0001,PGSE,Ecole d'Economie de Paris(2017), Groupement de Recherche et d'Etudes en Gestion à HEC (GREGH), ANR-19-CE26-0010,StratCom,Diffusion de l'information en présence de rationalité limitée et de canaux de transmission complexes(2019), ANR-11-IDEX-0003,IPS,Idex Paris-Saclay(2011), ANR-11-LABX-0047,ECODEC,Réguler l'économie au service de la société(2011), ANR-15-CE38-0007,CIGNE,Communication et Information dans des Jeux dans des Réseaux(2015), Théorie économique, modélisation et applications (THEMA), Université de Cergy Pontoise (UCP), Université Paris-Seine-Université Paris-Seine-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS), HEC Research Paper Series, and Université Panthéon-Sorbonne (UP1)-École normale supérieure - Paris (ENS Paris)-Institut National de la Recherche Agronomique (INRA)-École des hautes études en sciences sociales (EHESS)-École des Ponts ParisTech (ENPC)-Centre National de la Recherche Scientifique (CNRS)
Subjects: TheoryofComputation_MISCELLANEOUS, Computer Science::Computer Science and Game Theory, Class (set theory), Computer science, General Mathematics, Bayesian persuasion, Management Science and Operations Research, Outcome (game theory), Subgame perfect equilibrium, Strategy, Information design, 0502 economics and business, Converse, statistical experiments, 050207 economics, 050205 econometrics, Mathematics, 05 social sciences, Normal-form game, Sharing rules, Pareto principle, TheoryofComputation_GENERAL, Statistical experiments, [SHS.ECO]Humanities and Social Sciences/Economics and Finance, Computer Science Applications, Splitting games, Bayes correlated equilibrium, JEL: C - Mathematical and Quantitative Methods/C.C7 - Game Theory and Bargaining Theory/C.C7.C72 - Noncooperative Games, [SHS.GESTION]Humanities and Social Sciences/Business administration, 050206 economic theory, JEL: D - Microeconomics/D.D8 - Information, Knowledge, and Uncertainty/D.D8.D82 - Asymmetric and Private Information • Mechanism Design, Mathematical economics
Abstract: We study the interaction between multiple information designers who try to influence the behavior of a set of agents. When the set of messages available to each designer is finite, such games always admit subgame perfect equilibria. When designers produce public information about independent pieces of information, every equilibrium of the direct game (in which the set of messages coincides with the set of states) is an equilibrium with larger (possibly infinite) message sets. The converse is true for a class of Markovian equilibria only. When designers produce information for their own corporation of agents, pure strategy equilibria exist and are characterized via an auxiliary normal form game. In an infinite-horizon multi-period extension of information design games, a feasible outcome which Pareto dominates a more informative equilibrium of the one-period game is supported by an equilibrium of the multi-period game.
Published: 2022

12. Two-harmonic Periodic Disturbance Compensation for Dead-Time Processes with Online Identification of Input Delay

Author: Adam Peichl, Michal Kuchař, Can Kutlu Yuksel, Silviu-Iulian Niculescu, Tomáš Vyhlídal, Faculty of Mechanical Engineering [Prague] (CTU/FME), Czech Technical University in Prague (CTU), Laboratoire des signaux et systèmes (L2S), CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Dynamical Interconnected Systems in COmplex Environments (DISCO), Inria Saclay - Ile de France, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire des signaux et systèmes (L2S), CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Czech Science Foundation project No.21-07321S, Grant Agency of the Czech Technical University in Prague, student grants No. SGS21/152/OHK2/3T/12 and SGS20/159/OHK2/3T/12, Public grant overseen by the French National research Agency(ANR) as part of the Investissements d’Avenir program, through the 'ADI2020' project funded by the IDEX Paris-Saclay, ANR-11-IDEX-0003-02, and ANR-11-IDEX-0003,IPS,Idex Paris-Saclay(2011)
Subjects: delay estimation, Delay, time-varying delay, Control and Systems Engineering, frequency-domain, vibration control, [SPI.MECA.VIBR]Engineering Sciences [physics]/Mechanics [physics.med-ph]/Vibrations [physics.class-ph], [SPI.AUTO]Engineering Sciences [physics]/Automatic
Abstract: International audience; As in the case of the Smith predictor, when applied to dynamical systems with delay in the input, the stability of the internal model control (IMC) system can be very sensitive to the mismatch that can occur between the plant delay and the identified delay. In this paper, we propose an online identification technique for the plant with input delay, which is used to adapt an IMC controller designed to reject periodic disturbances consisting of two harmonics. The proposed method is based on wavelet analysis and cross-correlation of the measured output. Moreover, the proposed controller structure introduces a novel analytical approach which makes it suitable for the adaptive application. The practical motivation of the study is to address the delay mismatch that can be caused by approximating time-varying high-order systems by first-order models with input delay. The approach is numerically validated.
Published: 2022

13. Rolling Balance Board Robust Stabilization: A MID-based Design

Author: Amina BENARAB, Molnar, Csenge A., Islam Boussaada, Karim Trabelsi, Tamás Insperger, Silviu-Iulian Niculescu, BENARAB, Amina, Idex Paris-Saclay - - IPS2011 - ANR-11-IDEX-0003 - IDEX - VALID, Laboratoire des signaux et systèmes (L2S), CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Institut Polytechnique des Sciences Avancées (IPSA), Dynamical Interconnected Systems in COmplex Environments (DISCO), Inria Saclay - Ile de France, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire des signaux et systèmes (L2S), CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Budapest University of Technology and Economics [Budapest] (BME), and ANR-11-IDEX-0003,IPS,Idex Paris-Saclay(2011)
Subjects: [INFO.INFO-SY] Computer Science [cs]/Systems and Control [cs.SY], exponential stability, [MATH.MATH-GM] Mathematics [math]/General Mathematics [math.GM], [MATH] Mathematics [math], [SPI.AUTO]Engineering Sciences [physics]/Automatic, Multiplicity-Induced-Dominancy, [MATH.MATH-GM]Mathematics [math]/General Mathematics [math.GM], Human balance, [SPI.AUTO] Engineering Sciences [physics]/Automatic, Control and Systems Engineering, [INFO.INFO-SY]Computer Science [cs]/Systems and Control [cs.SY], [NLIN] Nonlinear Sciences [physics], [NLIN]Nonlinear Sciences [physics], [MATH]Mathematics [math]
Abstract: International audience; This paper considers the stabilization of a rolling balance board by means of the multiplicity-induceddominancy property. A two degree-of-freedom mechanical model of a human balancing on a rolling balance board is analyzed in the sagittal plane. The human body is modeled by an inverted pendulum which connects to the balance board through the ankle joint. The system is stabilized by the ankle torque managed by the central nervous system (CNS). The action of the CNS is modeled by a delayed full state feedback: a pointwise delay stands for all latencies in the neuromechanical system (reaction time, neuromechanical lag, etc.). The aim of the paper is to achieve a good occurrence in terms of the decay rate, it shows the links with dominancy and with the exponential stability property of the solution.
Published: 2022

14. Delay-difference Approximation of PD-Controllers. Insights into Improperly-posed Closed-loop Systems

Author: Torres-García, Diego, Méndez‐barrios, César‐fernando, Niculescu, Silviu-Iulian, Martínez-González, Alejandro, Dynamical Interconnected Systems in COmplex Environments (DISCO), Inria Saclay - Ile de France, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire des signaux et systèmes (L2S), CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Universidad Autonoma de San Luis Potosi [México] (UASLP), Laboratoire des signaux et systèmes (L2S), CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), IFAC, and ANR-11-IDEX-0003,IPS,Idex Paris-Saclay(2011)
Subjects: [SPI]Engineering Sciences [physics], Improperly-Posed Linear Systems, Control and Systems Engineering, PD-control, Delay-dependent Coefficients
Abstract: International audience; This paper focuses on the study of the behavior of critical roots when a dynamical system is stabilized by a PD-controller, for which the derivative action has been approximated by using two commensurate delays. The use of such an approximation leads to a characteristic quasipolynomial whose coefficients depend explicitly on the delay parameter. The aim of the paper is to address the way the delay parameter may affect the location of the roots of the corresponding characteristic function, and in particular the cases when "small" delays induce instability in the closed-loop systems. Such an analysis is performed by expressing the critical solution of the system as a delay-dependent power series. Illustrative examples complete the presentation.
Published: 2022

15. The hyperthermophilic archaeon Thermococcus kodakarensis is resistant to pervasive negative supercoiling activity of DNA gyrase

Author: Jacques Oberto, Ryan J. Catchpole, Tamara Basta, Patrick Forterre, Etienne Villain, Paul Villain, Violette Da Cunha, Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Département d'Immunologie - Department of Immunology, Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité), Virologie des archées - Archaeal Virology, Université Paris Cité (UPCité)-Microbiologie Intégrative et Moléculaire (UMR6047), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), University of Georgia [USA], ANR-11-EQPX-0029,MORPHOSCOPE 2,Imagerie et reconstruction multiéchelles de la morphogenèse. (Plateforme d'innovation technologique et méthodologique pour l'imagerie in vivo et la reconstruction des dynamiques multiéchelles de la morphogenèse)(2011), ANR-10-INBS-0004,France-BioImaging,Développment d'une infrastructure française distribuée coordonnée(2010), ANR-11-IDEX-0003,IPS,Idex Paris-Saclay(2011), and European Project: 340440,EC:FP7:ERC,ERC-2013-ADG,EVOMOBIL(2014)
Subjects: Hot Temperature, AcademicSubjects/SCI00010, DNA gyrase, Gene Expression Regulation, Enzymologic, chemistry.chemical_compound, Bacterial Proteins, Ciprofloxacin, Sequence Homology, Nucleic Acid, Genetics, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Thermotoga maritima, Molecular Biology, Gene, Microscopy, Confocal, Base Sequence, biology, DNA, Superhelical, Topoisomerase, biology.organism_classification, Anti-Bacterial Agents, Thermococcus kodakarensis, Thermococcus, DNA, Archaeal, chemistry, DNA Gyrase, Horizontal gene transfer, Biocatalysis, biology.protein, DNA supercoil, Gene Expression Regulation, Archaeal, DNA, Plasmids
Abstract: In all cells, DNA topoisomerases dynamically regulate DNA supercoiling allowing essential DNA processes such as transcription and replication to occur. How this complex system emerged in the course of evolution is poorly understood. Intriguingly, a single horizontal gene transfer event led to the successful establishment of bacterial gyrase in Archaea, but its emergent function remains a mystery. To better understand the challenges associated with the establishment of pervasive negative supercoiling activity, we expressed the gyrase of the bacterium Thermotoga maritima in a naïve archaeon Thermococcus kodakarensis which naturally has positively supercoiled DNA. We found that the gyrase was catalytically active in T. kodakarensis leading to strong negative supercoiling of plasmid DNA which was stably maintained over at least eighty generations. An increased sensitivity of gyrase-expressing T. kodakarensis to ciprofloxacin suggested that gyrase also modulated chromosomal topology. Accordingly, global transcriptome analyses revealed large scale gene expression deregulation and identified a subset of genes responding to the negative supercoiling activity of gyrase. Surprisingly, the artificially introduced dominant negative supercoiling activity did not have a measurable effect on T. kodakarensis growth rate. Our data suggest that gyrase can become established in Thermococcales archaea without critically interfering with DNA transaction processes., Graphical Abstract Graphical AbstractIntroduction of DNA gyrase in Thermococcus kodakarensis flips its DNA supercoiling from positive to negative with only mild effects on its cell physiology.
Published: 2021

16. X-ray imaging with Micromegas detectors with optical readout

Author: Cools, A., Aune, S., Beau, F., Brunbauer, F.M., Benoit, T., Desforge, D., Ferrer-Ribas, E., Kallitsopoulou, A., Malgorn, C., Oliveri, E., Papaevangelou, T., Pollacco, E.C., Ropelewski, L., Sari, A., Iguaz, F.J., Institut de Recherches sur les lois Fondamentales de l'Univers (IRFU), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Institut des Sciences du Vivant Frédéric JOLIOT (JOLIOT), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), CERN [Genève], Laboratoire Capteurs et Architectures Electroniques (LCAE), Département Métrologie Instrumentation & Information (DM2I), Laboratoire d'Intégration des Systèmes et des Technologies (LIST (CEA)), Direction de Recherche Technologique (CEA) (DRT (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Technologique (CEA) (DRT (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Laboratoire d'Intégration des Systèmes et des Technologies (LIST (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Synchrotron SOLEIL (SSOLEIL), Centre National de la Recherche Scientifique (CNRS), Cross-Disciplinary Program on Instrumentation and Detection (PTC-ID) of the French Alternative Energies and Atomic Energy Commission (CEA)., SOLEIL for provision of synchrotron radiation facilities (proposal number 99220033), RD51 at CERN, Weizmann Institute of Science, ANR-10-LABX-0038,P2IO,Physics of the 2 infinities and the origins(2010), and ANR-11-IDEX-0003,IPS,Idex Paris-Saclay(2011)
Subjects: Physics - Instrumentation and Detectors, neutron imaging, CMOS camera, FOS: Physical sciences, [PHYS.NEXP]Physics [physics]/Nuclear Experiment [nucl-ex], X-rays, synchrotron, beta-rays, cancer, [PHYS.PHYS.PHYS-INS-DET]Physics [physics]/Physics [physics]/Instrumentation and Detectors [physics.ins-det], Detectors and Experimental Techniques, physics.ins-det, nuclear instrumentation, instrumentation, detector, neutrons, Instrumentation and Detectors (physics.ins-det), gamma-rays, non-destructive examination, beta imaging, metrology, radioactivity, SOLEIL, ionizing radiation, radiography, Micromegas
Abstract: In the last years, optical readout of Micromegas gaseous detectors has been achieved by implementing a Micromegas detector on a glass anode coupled to a CMOS camera. Effective X-ray radiography was demonstrated using integrated imaging approach. High granularity values have been reached for low-energy X-rays from radioactive sources and X-ray generators. Detector characterization with X-ray radiography has led to two applications: neutron imaging for non-destructive examination of highly gamma-ray emitting objects and beta imaging for the single cell activity tagging in the field of oncology drug studies. First measurements investigating the achievable spatial resolution of the glass Micromegas detector at the SOLEIL synchrotron facility with a high-intensity and flat irradiation field will be shown in this article., Comment: 6 pages, 4 figures, 7th International Conference on Micro Pattern Gaseous Detectors, 11-16 December 20223, Weizmann Institute of Science, Rehovot, Israel
Published: 2022

17. Measure of the hygroscopic expansion of human dentin

Author: Gharbi, Hakim, Wenlong, Wang, Giraudet, Chloé, Allain, Jean-Marc, Vennat, Elsa, Laboratoire de mécanique des solides (LMS), École polytechnique (X)-Mines Paris - PSL (École nationale supérieure des mines de Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Mécanique Paris-Saclay (LMPS), CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Ecole Normale Supérieure Paris-Saclay (ENS Paris Saclay), Mathematical and Mechanical Modeling with Data Interaction in Simulations for Medicine (M3DISIM), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-École polytechnique (X)-Mines Paris - PSL (École nationale supérieure des mines de Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Inria Saclay - Ile de France, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Unité de Recherche Biomatériaux Innovants et Interfaces (URB2i (URP_4462)), Université Paris Cité (UPCité)-Université Sorbonne Paris Nord, This work has benefited from the financial support of the LabeX LaSIPS (ANR-10-LABX-0040-LaSIPS) managed by the French National Research Agency under the 'Investissements d'avenir' program (n°ANR-11-IDEX-0003-02)., and ANR-11-IDEX-0003,IPS,Idex Paris-Saclay(2011)
Subjects: DIC, Dentin, humidity, microscopy, FOS: Physical sciences, Medical Physics (physics.med-ph), strain measurement, mechanical properties, [PHYS.MECA.BIOM]Physics [physics]/Mechanics [physics]/Biomechanics [physics.med-ph], Physics - Medical Physics, compression
Abstract: Background: Direct dental restoration implies a drying of the dentin substrate. This drying may induce significant strain in the dentin, affecting the bonding efficiency of the restoration. Objective: We measure the dilatation of dentine under changes of relative humidity as well as the impact of humidity on dentin elastic properties. This investigates the role of relative humidity variation during dental surgery on restoration lifetime. Methods: We have coupled an environmental chamber to control both temperature and humidity on the sample, with an optical microscope to measure precisely the strain on the sample surface, after a quantification of the measurement noise. This set-up is used on carefully prepared samples placed on a compression device to measure the elastic parameters. Results: Dentin dilates when the relative humidity increases, with a coefficient of hygroscopic expansion of typically 6.10-3 %.(%RH)-1. This dilatation occurs in about ten minutes. Young modulus and Poisson's ratio are not modified by the variation of relative humidity. Conclusions: Hygroscopic expansion is an order of magnitude larger than thermal expansion during dental surgery: around 0.3% with respect to 0.03%. These levels are low with respect to dental rupture, but may induce a significant decrease of the life-expectancy of a restoration.
Published: 2022

18. The transcriptional co-regulators NBCL1 and NBCL2 redundantly coordinate aerial organ development and root nodule identity in legumes

Author: Shengbin Liu, Kévin Magne, Jing Zhou, Juliette Laude, Marion Dalmais, Christine Le Signor, Abdelhafid Bendahmane, Richard Thompson, Jean-Malo Couzigou, Pascal Ratet, Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Agroécologie [Dijon], Université de Bourgogne (UB)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Dijon, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), This work was supported by the Centre National de la RechercheScientifique (CNRS) and by a grant from the French National ResearchAgency (ANR-14-CE19-0003-01) to PR. This work has benefittedfrom the support of the French Laboratory of Excellence (Labex) SaclayPlant Sciences (ANR-10-LABX-0040-SPS, LabEx SPS and ANR-17-EUR-0007, EUR SPS-GSR) which is managed by the French NationalResearch Agency under the program ‘Investissements d’avenir’ (ANR-11-IDEX-0003-02). J-MC and JZ were supported by the FrenchLaboratory of Excellence (Labex) project ‘TULIP’ (ANR-10-LABX-41, ANR-11-IDEX-0002-02), ANR-14-CE19-0003,NOOT,Les gènes NOOT gardiens de l'dentité des nodosités symbiotiques et de l'abscission(2014), ANR-10-LABX-0040,SPS,Saclay Plant Sciences(2010), ANR-11-IDEX-0003,IPS,Idex Paris-Saclay(2011), and ANR-11-IDEX-0002,UNITI,Université Fédérale de Toulouse(2011)
Subjects: NODULE-ROOT, Physiology, [SDV]Life Sciences [q-bio], Plant Science, organ identity, symbiosis, stipule, Medicago truncatula, inflorescence, COCHLEATA, development, boundaries, Pisum sativum, NOOT-BOP-COCH-LIKE
Abstract: International audience; Medicago truncatula NODULE ROOT1 (MtNOOT1) and Pisum sativum COCHLEATA1 (PsCOCH1) are orthologous genes belonging to the NOOT-BOP-COCH-LIKE (NBCL) gene family which encodes key transcriptional co-regulators of plant development. In Mtnoot1 and Pscoch1 mutants, the development of stipule, flower and symbiotic nodules is altered. MtNOOT2 and PsCOCH2 represent the single paralogs of MtNOOT1 and PsCOCH1, respectively. In M. truncatula, MtNOOT1 and MtNOOT2 are both required for the establishment and maintenance of the symbiotic nodule identity. In contrast to the NBCL1 genes, the role of NBCL2 genes in legume above-ground development is not known. To better understand the roles of NBCL genes in legumes, we used M. truncatula and P. sativum nbcl mutants from the literature, isolated a knockout mutant for the PsCOCH2 locus and generated Pscoch1coch2 double mutants in P. sativum. These new mutant lines enabled to compare the roles of MtNOOT2 and PsCOCH2 in both M. truncatula and P. sativum legume development. Our work shows that the single Mtnoot2 and Pscoch2 mutants develop wild-type stipules, flowers and symbiotic nodules. However, the number of flowers was increased and the pods and seeds were smaller in comparison to wild type. Furthermore, in comparison to the corresponding nbcl1 single mutants, both the M. truncatula and P. sativum nbcl double mutants show a drastic alteration in stipule, inflorescence, flower and nodule development. Remarkably, in both M. truncatula and P. sativum nbcl double mutants, stipules are transformed into a range of aberrant leaf-like structures.
Published: 2022

19. New Features of P3δ Software. Insights and Demos

Author: Boussaada, Islam, Mazanti, Guilherme, Niculescu, Silviu-Iulian, Hammoumou, Ayrton, Millet, Titouan, Raj, Jayvir, Huynh, Julien, Institut Polytechnique des Sciences Avancées (IPSA), Laboratoire des signaux et systèmes (L2S), CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Dynamical Interconnected Systems in COmplex Environments (DISCO), Inria Saclay - Ile de France, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire des signaux et systèmes (L2S), CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), and ANR-11-IDEX-0003,IPS,Idex Paris-Saclay(2011)
Subjects: Control and Systems Engineering, Optimization and Control (math.OC), delay, GUI, FOS: Mathematics, online software, [MATH.MATH-OC]Mathematics [math]/Optimization and Control [math.OC], stability, Mathematics - Optimization and Control, controller design, Python toolbox
Abstract: This paper presents the software entitled "Partial Pole Placement via Delay Action", or "P3$\delta$" for short. P3$\delta$ is a Python software with a friendly user interface for the design of parametric stabilizing feedback laws with time-delays for dynamical systems. After recalling the theoretical foundation of the so-called "Partial Pole Placement" methodology we propose as well the main features of the current version of P3$\delta$. We illustrate its use in feedback stabilization of several control systems operating under time delays., Comment: arXiv admin note: text overlap with arXiv:2107.11341
Published: 2022

20. Counting Characteristic Roots of Linear Delay Differential Equations. Part II: from Argument Principle to Rightmost Root Assignment Methods

Author: Silviu-Iulian Niculescu, Islam Boussaada, Dynamical Interconnected Systems in COmplex Environments (DISCO), Inria Saclay - Ile de France, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire des signaux et systèmes (L2S), CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Laboratoire des signaux et systèmes (L2S), CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Institut Polytechnique des Sciences Avancées (IPSA), This work is supported by a public grant overseen by the French National Research Agency (ANR) as part of the 'Investissement d’Avenir' program, through the iCODE project funded by the IDEX Paris-Saclay, ANR-11-IDEX-0003-02., and ANR-11-IDEX-0003,IPS,Idex Paris-Saclay(2011)
Subjects: [MATH]Mathematics [math]
Abstract: International audience; This chapter briefly presents some "user-friendly" methods and techniques (frequency-domain approaches) for the analysis and control of linear dynamical systems in presence of delays. The presentation is as simple as possible, focusing more on the main intuitive (algebraic, geometric) ideas to develop theoretical results, and their potential use in practical applications. To fix better the ideas, scalar and second-order examples are largely discussed. Next, a particular attention will be paid to the existing links between the maximal allowable multiplicity of the characteristic roots and the spectral abscissa of the dynamical system. The underlying property-multiplicity induced dominancy-will be particularly useful in constructing low-complexity controllers by partial pole placement. Such an idea is particularly exploited in vibration control.
Published: 2022

21. A chromosome-level, haplotype-phased Vanilla planifolia genome highlights the challenge of partial endoreplication for accurate whole-genome assembly

Author: Piet, Quentin, Droc, Gaetan, Marande, William, Sarah, Gautier, Bocs, Stéphanie, Klopp, Christophe, Bourge, Mickael, Siljak-Yakovlev, Sonja, Bouchez, Olivier, Lopez-Roques, Céline, Lepers-Andrzejewski, Sandra, Bourgois, Laurent, Zucca, Joseph, Dron, Michel, Besse, Pascale, Grisoni, Michel, Jourda, Cyril, Charron, Carine, Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de La Réunion (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), South Green Bioinformatics Platform [Montpellier], Centre National de Ressources Génomiques Végétales (CNRGV), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Plateforme Bio-Informatique - Génotoul, Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRAE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-BioInfOmics, Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRAE), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Ecologie Systématique et Evolution (ESE), AgroParisTech-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Génome et Transcriptome - Plateforme Génomique ( GeT-PlaGe), Plateforme Génome & Transcriptome (GET), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Etablissement public Vanille de Tahiti, Eurovanille, V. Mane Fils, 620 route de Grasse, 06620 Le Bar sur Loup, France., Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), This work was supported by grants from Eurovanille and V. Mane Fils companies. The research was co-funded by the Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), the Université de La Réunion (UR), the Institut National de Recherche pour l’Agriculture l’Alimentation et l’Environnement (INRAE), the Centre National de la Recherche Scientifique (CNRS), and the Etablissement Vanille de Tahiti (EVT). This work was also supported by grants from the European Regional Development Fund (ERDF), the Conseil Régional de la Réunion, and the Conseil Départemental de la Réunion. This work was supported by France Génomique National infrastructure, funded as part of 'Investissement d’avenir' program managed by Agence Nationale pour la Recherche (ANR-10-INBS-0009, France Génomique) and has also benefited from Imagerie-Gif core facility, supported by l’Agence Nationale de la Recherche (ANR-11-EQPX-0029 Morphoscope 2, ANR-10-INBS-04 France BioImaging, ANR-11-IDEX-0003-02 IDEX Paris-Saclay)., ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), ANR-11-EQPX-0029,MORPHOSCOPE 2,Imagerie et reconstruction multiéchelles de la morphogenèse. (Plateforme d'innovation technologique et méthodologique pour l'imagerie in vivo et la reconstruction des dynamiques multiéchelles de la morphogenèse)(2011), ANR-10-INBS-0004,France-BioImaging,Développment d'une infrastructure française distribuée coordonnée(2010), and ANR-11-IDEX-0003,IPS,Idex Paris-Saclay(2011)
Subjects: optical mapping, Genome Size, Haplotypes, partial endoreplication, vanilla, whole-genome sequencing, [SDV]Life Sciences [q-bio], genome hub, Endoreduplication, Chromosomes
Abstract: International audience; Vanilla planifolia, the species cultivated to produce one of the world’s most popular flavors, is highly prone to partial genome endoreplication, which leads to highly unbalanced DNA content in cells. We report here the first molecular evidence of partial endoreplication at the chromosome scale by the assembly and annotation of an accurate haplotype-phased genome of V. planifolia. Cytogenetic data demonstrated that the diploid genome size is 4.09 Gb, with 16 chromosome pairs, although aneuploid cells are frequently observed. Using PacBio HiFi and optical mapping, we assembled and phased a diploid genome of 3.4 Gb with a scaffold N50 of 1.2 Mb and 59 128 predicted protein-coding genes. The atypical k-mer frequencies and the uneven sequencing depth observed agreed with our expectation of unbalanced genome representation. Sixty-seven percent of the genes were scattered over only 30% of the genome, putatively linking gene-rich regions and the endoreplication phenomenon. By contrast, low-coverage regions (non-endoreplicated) were rich in repeated elements but also contained 33% of the annotated genes. Furthermore, this assembly showed distinct haplotype-specific sequencing depth variation patterns, suggesting complex molecular regulation of endoreplication along the chromosomes. This high-quality, anchored assembly represents 83% of the estimated V. planifolia genome. It provides a significant step toward the elucidation of this complex genome. To support post-genomics efforts, we developed the Vanilla Genome Hub, a user-friendly integrated web portal that enables centralized access to high-throughput genomic and other omics data and interoperable use of bioinformatics tools.
Published: 2022

22. Structural and Large-scale Analysis Unveil the Intertwined Paths Promoting NMT-catalyzed Lysine and Glycine Myristoylation

Author: Cyril Dian, Frédéric Riviere, Thierry Meinnel, Carmela Giglione, Rémi DUTHEIL, Paul Monassa, Maturation des proteines, destinée cellulaire et thérapeutique (PROMTI), Département Biologie des Génomes (DBG), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), ARCPJA32020060002137, Fondation pour la Recherche Médicale (FDT202001010779), Région Ile-de-France (17012695), ANR-20-CE44-0013,DynaMYT,Une combinaison de nouveaux outils chimiques pour élucider la dynamique du Myristome(2020), ANR-11-IDEX-0003,IPS,Idex Paris-Saclay(2011), and ANR-10-INBS-0005,FRISBI,Infrastructure Française pour la Biologie Structurale Intégrée(2010)
Subjects: [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Acylation, myristoylation, Lysine, Glycine, Myristic Acid, Catalysis, N-terminal modification, Kinetics, Structural Biology, Humans, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], Molecular Biology, Protein Processing, Post-Translational, N-myristoyltransferase, Acyltransferases
Abstract: International audience; N-myristoyltransferases (NMTs) catalyze protein myristoylation, a lipid modification crucial for cell survival and a range of pathophysiological processes. Originally thought to modify only N-terminal glycine α-amino groups (G-myristoylation), NMTs were recently shown to also modify lysine ε-amino groups (K-myristoylation). However, the clues ruling NMTdependent K-myristoylation and the full range of targets are currently unknown. Here we combine mass spectrometry, kinetic studies, in silico analysis, and crystallography to identify the specific features driving each modification. We show that direct interactions between the substrate's reactive amino group and the NMT catalytic base promote K-myristoylation but with poor efficiency compared to G-myristoylation, which instead uses a water-mediated interaction. We provide evidence of depletion of proteins with NMT-dependent Kmyristoylation motifs in humans, suggesting evolutionary pressure to prevent this modification in favor of G-myristoylation. In turn, we reveal that K-myristoylation may only result from post-translational events. Our studies finally unravel the respective paths towards Kmyristoylation or G-myristoylation, which rely on a very subtle tradeoff embracing the chemical landscape around the reactive group.
Published: 2022

23. Do syntactic trees enhance Bidirectional Encoder Representations from Transformers (BERT) models for chemical–drug relation extraction?

Author: Anfu, Tang, Louise, Deléger, Robert, Bossy, Pierre, Zweigenbaum, Claire, Nédellec, Mathématiques et Informatique Appliquées du Génome à l'Environnement [Jouy-En-Josas] (MaIAGE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Information, Langue Ecrite et Signée (ILES), Laboratoire Interdisciplinaire des Sciences du Numérique (LISN), Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Sciences et Technologies des Langues (STL), Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), ANR-11-LABX-0045,DIGICOSME,Mondes numériques: Données, programmes et architectures distribués(2011), and ANR-11-IDEX-0003,IPS,Idex Paris-Saclay(2011)
Subjects: [INFO.INFO-TT]Computer Science [cs]/Document and Text Processing, Biomedical Research, Databases, Factual, Data Mining, General Agricultural and Biological Sciences, General Biochemistry, Genetics and Molecular Biology, [INFO.INFO-CL]Computer Science [cs]/Computation and Language [cs.CL], Natural Language Processing, Semantics, Information Systems
Abstract: Collecting relations between chemicals and drugs is crucial in biomedical research. The pre-trained transformer model, e.g. Bidirectional Encoder Representations from Transformers (BERT), is shown to have limitations on biomedical texts; more specifically, the lack of annotated data makes relation extraction (RE) from biomedical texts very challenging. In this paper, we hypothesize that enriching a pre-trained transformer model with syntactic information may help improve its performance on chemical–drug RE tasks. For this purpose, we propose three syntax-enhanced models based on the domain-specific BioBERT model: Chunking-Enhanced-BioBERT and Constituency-Tree-BioBERT in which constituency information is integrated and a Multi-Task-Learning framework Multi-Task-Syntactic (MTS)-BioBERT in which syntactic information is injected implicitly by adding syntax-related tasks as training objectives. Besides, we test an existing model Late-Fusion which is enhanced by syntactic dependency information and build ensemble systems combining syntax-enhanced models and non-syntax-enhanced models. Experiments are conducted on the BioCreative VII DrugProt corpus, a manually annotated corpus for the development and evaluation of RE systems. Our results reveal that syntax-enhanced models in general degrade the performance of BioBERT in the scenario of biomedical RE but improve the performance when the subject–object distance of candidate semantic relation is long. We also explore the impact of quality of dependency parses. [Our code is available at: https://github.com/Maple177/syntax-enhanced-RE/tree/drugprot (for only MTS-BioBERT); https://github.com/Maple177/drugprot-relation-extraction (for the rest of experiments)] Database URL https://github.com/Maple177/drugprot-relation-extraction
Published: 2022

24. Analysis of morphological and physicochemical changes in space-weathered hydrated silicates by visible/IR spectroscopy and electron transmission microscopy

Author: Rubino, S., Leroux, H., Aleon-Toppani, A., Lantz, C., Baklouti, D., Djouadi, Z., Troadec, David, Borondics, F., Brunetto, R., Institut d'astrophysique spatiale (IAS), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Centre National d’Études Spatiales [Paris] (CNES), Unité Matériaux et Transformations - UMR 8207 (UMET), Centrale Lille-Institut de Chimie du CNRS (INC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut d’Électronique, de Microélectronique et de Nanotechnologie - UMR 8520 (IEMN), Centrale Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université Polytechnique Hauts-de-France (UPHF)-JUNIA (JUNIA), Université catholique de Lille (UCL)-Université catholique de Lille (UCL), Centrale de Micro Nano Fabrication - IEMN (CMNF - IEMN), Université catholique de Lille (UCL)-Université catholique de Lille (UCL)-Centrale Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université Polytechnique Hauts-de-France (UPHF)-JUNIA (JUNIA), Synchrotron SOLEIL (SSOLEIL), Centre National de la Recherche Scientifique (CNRS), We thank O. Mivumbi, D. Ledu, C.O. Bacri, and P. Benoit-Lamaitrie for help and technical support with SIDONIE and INGMAR. INGMAR is a joint IAS-CSNSM (Orsay, France) facility funded by the P2IO LabEx (ANR-10-LABX-0038) in the framework Investissements d'Avenir (ANR-11-IDEX-0003-01). Finally, we thank A. Fadel for help and technical support with the SEM acquisitions. This work has been funded by the ANR project CLASSY (Grant ANR-17-CE31-0004-02)., Renatech Network, CMNF, ANR-10-LABX-0038,P2IO,Physics of the 2 infinities and the origins(2010), ANR-11-IDEX-0003,IPS,Idex Paris-Saclay(2011), and ANR-17-CE31-0004,CLASSY,Composition des surfaces du Système Solaire de bas albédo(2017)
Subjects: [SPI]Engineering Sciences [physics]
Abstract: International audience
Published: 2022

25. SeSAM: software for automatic construction of order-robust linkage maps

Author: Adrien Vidal, Franck Gauthier, Willy Rodrigez, Nadège Guiglielmoni, Damien Leroux, Nicolas Chevrolier, Sylvain Jasson, Elise Tourrette, Olivier C. Martin, Matthieu Falque, Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) (GQE-Le Moulon), AgroParisTech-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRAE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), MARS-WRIGLEY co-funded the salary of AV and WR. The funding bodies did not play any role in the design of the study, collection, analysis, and interpretation of the data, or writing the manuscript., ANR-10-LABX-0040,SPS,Saclay Plant Sciences(2010), ANR-11-IDEX-0003,IPS,Idex Paris-Saclay(2011), ANR-10-BTBR-0001,AMAIZING,Développer de nouvelles variétés de maïs pour une agriculture durable: une approche intégrée de la génomique à la sélection(2010), and Université Paris-Saclay
Subjects: Genetic Markers, [SDV.GEN]Life Sciences [q-bio]/Genetics, Genotype, Linkage, Applied Mathematics, Chromosome Mapping, Genetic mapping, Biochemistry, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Polymorphism, Single Nucleotide, Computer Science Applications, Genetic mapping Linkage Automated software Seriation Marker order robustness, Automated software, Marker order robustness, Structural Biology, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Seriation, Molecular Biology, Software
Abstract: Background Genotyping and sequencing technologies produce increasingly large numbers of genetic markers with potentially high rates of missing or erroneous data. Therefore, the construction of linkage maps is more and more complex. Moreover, the size of segregating populations remains constrained by cost issues and is less and less commensurate with the numbers of SNPs available. Thus, guaranteeing a statistically robust marker order requires that maps include only a carefully selected subset of SNPs. Results In this context, the SeSAM software allows automatic genetic map construction using seriation and placement approaches, to produce (1) a high-robustness framework map which includes as many markers as possible while keeping the order robustness beyond a given statistical threshold, and (2) a high-density total map including the framework plus almost all polymorphic markers. During this process, care is taken to limit the impact of genotyping errors and of missing data on mapping quality. SeSAM can be used with a wide range of biparental populations including from outcrossing species for which phases are inferred on-the-fly by maximum-likelihood during map elongation. The package also includes functions to simulate data sets, convert data formats, detect putative genotyping errors, visualize data and map quality (including graphical genotypes), and merge several maps into a consensus. SeSAM is also suitable for interactive map construction, by providing lower-level functions for 2-point and multipoint EM analyses. The software is implemented in a R package including functions in C++. Conclusions SeSAM is a fully automatic linkage mapping software designed to (1) produce a framework map as robust as desired by optimizing the selection of a subset of markers, and (2) produce a high-density map including almost all polymorphic markers. The software can be used with a wide range of biparental mapping populations including cases from outcrossing. SeSAM is freely available under a GNU GPL v3 license and works on Linux, Windows, and macOS platforms. It can be downloaded together with its user-manual and quick-start tutorial from ForgeMIA (SeSAM project) at https://forgemia.inra.fr/gqe-acep/sesam/-/releases
Published: 2022

26. Dynamic analysis of confined ionic liquids and ionic magnetic fluids: highlighting long range elastic interactions

Author: Kume, Eni, Dunne, Peter, Martin, Nicolas, Baroni, Patrick, Noirez, Laurence, LLB - Nouvelles frontières dans les matériaux quantiques (NFMQ), Laboratoire Léon Brillouin (LLB - UMR 12), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), ANR-10-LABX-0039,PALM,Physics: Atoms, Light, Matter(2010), ANR-11-IDEX-0003,IPS,Idex Paris-Saclay(2011), and European Project: 766007,MAMI
Subjects: ionic liquids, mechanical measurements, shear elasticity, neutron scattering, Soft Condensed Matter (cond-mat.soft), FOS: Physical sciences, Condensed Matter - Soft Condensed Matter, [PHYS.COND.CM-SCM]Physics [physics]/Condensed Matter [cond-mat]/Soft Condensed Matter [cond-mat.soft]
Abstract: By reinforcing the interaction energy of the liquid with respect to the surface using total wetting boundary conditions, the response of liquids to mechanical shear stress is stronger and exhibits at sub-millimeter scale elastic properties. This study extends here to liquids with strong electrostatic interactions such as ionic liquids and paramagnetic liquids. We show that it is also possible to identify and measure a non-zero low-frequency shear elasticity at sub-millimeter scale. The observation of mesoscopic elastic properties in liquids generally considered as viscous away from any phase transition and the absence of extended structuring confirm the relevance of considering elastic interactions as contributing to collective effects under external electric or magnetic field.
Published: 2022

27. DETECTION OF METHANE PLUMES IN HYPERSPECTRAL IMAGES FROM SENTINEL-5P BY COUPLING ANOMALY DETECTION AND PATTERN RECOGNITION

Author: E. Ouerghi, T. Ehret, C. de Franchis, G. Facciolo, T. Lauvaux, E. Meinhardt, J.-M. Morel, Ecole Normale Supérieure Paris-Saclay (ENS Paris Saclay), Kayrros, Laboratoire des Sciences du Climat et de l'Environnement [Gif-sur-Yvette] (LSCE), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), ANR-11-IDEX-0003,IPS,Idex Paris-Saclay(2011), ANR-17-ASTR-0013,Filmer la Terre en relief,Filmer la Terre en relief : Reconstruction 3D et détection de changement(2017), and ANR-17-MPGA-0008,CIUDAD,Quantification of urban greenhouse gas emissions(2017)
Subjects: Background subtraction, Technology, Time series, Pixel, Anomaly (natural sciences), Hyperspectral imaging, Anomaly detection, Albedo, Engineering (General). Civil engineering (General), Constant false alarm rate, TA1501-1820, Hyperspectral, [SDU]Sciences of the Universe [physics], Pattern recognition, Principal component analysis, A contrario modeling, Environmental science, Applied optics. Photonics, TA1-2040, Methane, Remote sensing
Abstract: XXIV ISPRS Congress (2021 edition); International audience; Reducing methane emissions is essential to tackle climate change. Here, we address the problem of detecting large methane leaks using hyperspectral data from the Sentinel-5P satellite. For that we exploit the fine spectral sampling of Sentinel-5P data to detect methane absorption features visible in the shortwave infrared wavelength range (SWIR). Our method involves three separate steps: i) background subtraction, ii) detection of local maxima in the negative logarithmic spectrum of each pixel and iii) anomaly detection in the background-free image. In the first step, we remove the impact of the albedo using albedo maps and the impact of the atmosphere by using a principal component analysis (PCA) over a time series of past observations. In the second step, we count for each pixel the number of local maxima that correspond to a subset of local maxima in the methane absorption spectrum. This counting method allows us to set up a statistical a contrario test that controls the false alarm rate of our detections. In the last step we use an anomaly detector to isolate potential methane plumes and we intersect those potential plumes with what have been detected in the second step. This process strongly reduces the number of false alarms. We validate our method by comparing the detected plumes against a dataset of plumes manually annotated on the Sentinel-5P L2 methane product.
Published: 2021

28. A highly efficient solution and solid state ESIPT fluorophore and its OLED application

Author: Pei Yu, Sophie Gadan, Sandra Mazerat, Bernard Geffroy, Gilles Clavier, Anne Léaustic, Clémence Allain, Virgile Trannoy, Régis Guillot, Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), Institut de Chimie du CNRS (INC)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Photophysique et Photochimie Supramoléculaires et Macromoléculaires (PPSM), Institut de Chimie du CNRS (INC)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Ecole Normale Supérieure Paris-Saclay (ENS Paris Saclay), Laboratoire Innovation en Chimie des Surfaces et NanoSciences (LICSEN), Nanosciences et Innovation pour les Matériaux, la Biomédecine et l'Energie (ex SIS2M) (NIMBE UMR 3685), Institut Rayonnement Matière de Saclay (IRAMIS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Institut Rayonnement Matière de Saclay (IRAMIS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), Laboratoire de physique des interfaces et des couches minces [Palaiseau] (LPICM), École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS), ANR-11-IDEX-0003,IPS,Idex Paris-Saclay(2011), Laboratoire Innovation en Chimie des Surfaces et NanoSciences (LICSEN UMR 3685), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut Rayonnement Matière de Saclay (IRAMIS), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Fluorophore, Proton, 010405 organic chemistry, Chemistry, Hydrogen bond, [CHIM.MATE]Chemical Sciences/Material chemistry, General Chemistry, Electroluminescence, 010402 general chemistry, 01 natural sciences, Fluorescence, Catalysis, 0104 chemical sciences, chemistry.chemical_compound, Crystallography, Intramolecular force, Excited state, Materials Chemistry, OLED
Abstract: We present herein the synthesis and the photophysics of 2,2’-bipyridine-3,3’-diol-5,5’-dicarboxylic acid ethyl ester (BP(OH)$_2$DCEt$_2$), an excited state intramolecular proton tranfer (ESIPT)-based fluorophore featuring two identical intramolecular hydrogen bonds. BP(OH)$_2$DCEt$_2$ emits efficiently not only in solution, including protic solvents ($\lambda _{em}$ = 521 nm, $\Phi$$_f$ = 40 to 75%), but also in crystalline state ($\lambda _{em}$ = 530 nm, $\Phi$$_f$ = 51%). In addition, its saponified form (Na2BP(OH)2DC) is highly fluorescent in water ($\lambda _{em}$ = 490 nm, $\Phi$$_f$ = 51%). Finally, the good electroluminescence performance of BP(OH)$_2$DCEt$_2$ is also demonstrated in an OLED device.
Published: 2021
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29. CD38‐NADase is a new major contributor to Duchenne muscular dystrophic phenotype

Author: Antoine de Zélicourt, Abdallah Fayssoil, Mbarka Dakouane‐Giudicelli, Isley De Jesus, Ahmed Karoui, Faouzi Zarrouki, Florence Lefebvre, Arnaud Mansart, Jean‐Marie Launay, Jerome Piquereau, Mariana G Tarragó, Marcel Bonay, Anne Forand, Sophie Moog, France Piétri‐Rouxel, Elise Brisebard, Claudia C S Chini, Sonu Kashyap, Matthew J Fogarty, Gary C Sieck, Mathias Mericskay, Eduardo N Chini, Ana Maria Gomez, José‐Manuel Cancela, Sabine de la Porte, Institut des Neurosciences Paris-Saclay (NeuroPSI), Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Handicap neuromusculaire : Physiopathologie, Biothérapie et Pharmacologies appliquées (END-ICAP), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Institut National de la Santé et de la Recherche Médicale (INSERM), Signalisation et physiopathologie cardiovasculaire (CARPAT), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Saclay, Infection et inflammation (2I), Marqueurs cardiovasculaires en situation de stress (MASCOT (UMR_S_942 / U942)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Groupe Hospitalier Saint Louis - Lariboisière - Fernand Widal [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Université Sorbonne Paris Nord, Mayo Clinic [Rochester], Centre de recherche en Myologie – U974 SU-INSERM, Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), École nationale vétérinaire, agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS), BABARIT, Candice, Blanc 2013 - Arythmies dépendantes du calcium intracellulaire : mécanismes de la tachycardie ventriculaire catécholergique. - - ARyRthmia2013 - ANR-13-BSV1-0023 - Blanc 2013 - VALID, Idex Paris-Saclay - - IPS2011 - ANR-11-IDEX-0003 - IDEX - VALID, Mécanismes proarythmiques dépendant du sodium et du calcium - - NaCaR2019 - ANR-19-CE14-0031 - AAPG2019 - VALID, Université de Versailles Saint-Quentin-en-Yvelines - UFR Sciences de la santé Simone Veil (UVSQ Santé), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Physiopathologie Animale et bioThérapie du muscle et du système nerveux (PAnTher), École nationale vétérinaire, agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Expertise en Anatomie Pathologique (APEX), École nationale vétérinaire, agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-École nationale vétérinaire, agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Mayo Clinic, This research has been supported by grants from CNRS, INSERM, and Paris-Saclay University. Funding for this work was provided by AFM-telethon grants(JMC, SDP, and AZ). AZ is a recipient of a PhD fellowship from the Paris-SudUniversity. This work was also partly funded by the Fondation de France (JMC),ANRs (NAD-Heart #17-CE17-0015-01to MM, and ANR-19-CE14-0031-01andANR-13-BSV1-0023-01to AMG), and NIH AG58812to ENC. INSERM U1180is amember of the Laboratory of Excellence LERMIT supported by a grant fromANR (ANR-10-LABX-33) under the program'Investissements d’Avenir'ANR-11-IDEX-0003-01. The authors thank the radiology department of the RaymondPoincare Hospital. The authors thank Sanofi for providing isatuximab. Theauthors thank Frances Lund for providing CD38/mice and the platform forimmortalization of human cells'MyoLine'from the Institut of Myology forproviding the DMD and healthy subject cell lines. Graphical abstract has beencreated with BioRender.com.ENC, J-MC, SP, and AZ have patents on the use of CD38inhibitors, ANR-13-BSV1-0023,ARyRthmia,Arythmies dépendantes du calcium intracellulaire : mécanismes de la tachycardie ventriculaire catécholergique.(2013), ANR-11-IDEX-0003,IPS,Idex Paris-Saclay(2011), and ANR-19-CE14-0031,NaCaR,Mécanismes proarythmiques dépendant du sodium et du calcium(2019)
Subjects: calcium, [SDV]Life Sciences [q-bio], NAD, ADP-ribosyl Cyclase 1, [SDV] Life Sciences [q-bio], Muscular Dystrophy, Duchenne, Mice, NAD+ Nucleosidase, Phenotype, NAD+, DMD, Mice, Inbred mdx, Animals, Humans, Molecular Medicine, Myocytes, Cardiac, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Muscle, Skeletal, cardiomyopathy, CD38, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology
Abstract: ENC, J-MC, SP, and AZ have patents on the use of CD38inhibitors ENC, J-MC, SP, and AZ have patents on the use of CD38inhibitors ENC, J-MC, SP, and AZ have patents on the use of CD38inhibitors; International audience; Duchenne muscular dystrophy (DMD) is characterized by progressive muscle degeneration. Two important deleterious features are a Ca2+ dysregulation linked to Ca2+ influxes associated with ryanodine receptor hyperactivation, and a muscular nicotinamide adenine dinucleotide (NAD+ ) deficit. Here, we identified that deletion in mdx mice of CD38, a NAD+ glycohydrolase-producing modulators of Ca2+ signaling, led to a fully restored heart function and structure, with skeletal muscle performance improvements, associated with a reduction in inflammation and senescence markers. Muscle NAD+ levels were also fully restored, while the levels of the two main products of CD38, nicotinamide and ADP-ribose, were reduced, in heart, diaphragm, and limb. In cardiomyocytes from mdx/CD38-/- mice, the pathological spontaneous Ca2+ activity was reduced, as well as in myotubes from DMD patients treated with isatuximab (SARCLISA® ) a monoclonal anti-CD38 antibody. Finally, treatment of mdx and utrophin-dystrophin-deficient (mdx/utr-/- ) mice with CD38 inhibitors resulted in improved skeletal muscle performances. Thus, we demonstrate that CD38 actively contributes to DMD physiopathology. We propose that a selective anti-CD38 therapeutic intervention could be highly relevant to develop for DMD patients.
Published: 2022

30. DNA Methylation in Ensifer Species during Free-Living Growth and during Nitrogen-Fixing Symbiosis with Medicago spp

Author: Alessio Mengoni, Nicole Shapiro, Matthew J. Blow, Peter Mergaert, Tanja Woyke, Quentin Nicoud, Emanuele G. Biondi, Benoit Alunni, Janis H.T. Cheng, Lisa Cangioli, George C. diCenzo, Bulgarelli, Davide, Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Queen's University [Kingston, Canada], University of California [Berkeley] (UC Berkeley), University of California (UC), DOE Joint Genome Institute [Walnut Creek], Department of Energy / Joint Genome Institute (DOE), Los Alamos National Laboratory (LANL), Laboratoire de chimie bactérienne (LCB), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Università degli Studi di Firenze = University of Florence (UniFI), ANR-11-EQPX-0029,MORPHOSCOPE 2,Imagerie et reconstruction multiéchelles de la morphogenèse. (Plateforme d'innovation technologique et méthodologique pour l'imagerie in vivo et la reconstruction des dynamiques multiéchelles de la morphogenèse)(2011), ANR-11-IDEX-0003,IPS,Idex Paris-Saclay(2011), ANR-17-CE20-0011,SymbiontCellCyc,Rôle du cycle cellulaire bactérien dans la fixation symbiotique d'azote chez les Légumineuses(2017), Università degli Studi di Firenze = University of Florence [Firenze] (UNIFI), I2BC - Institut de Biologie Intégrative de la Cellule, Institute for Integrative Biology of the Cell [Gif-sur-Yvette] (I2BC), and Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.
Subjects: symbiotic nitrogen fixation, Methyltransferase, Physiology, [SDV]Life Sciences [q-bio], 1.1 Normal biological development and functioning, Cell, Biology, rhizobia, Biochemistry, Microbiology, DNA sequencing, 03 medical and health sciences, Underpinning research, CcrM, medicine, Genetics, Endoreduplication, 2.2 Factors relating to the physical environment, Replicon, Aetiology, Molecular Biology, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, 0303 health sciences, DNA methylation, 030306 microbiology, Human Genome, fungi, Cell cycle regulation, Rhizobia, Symbiotic nitrogen fixation, food and beverages, Methylation, Cell cycle, Computer Science Applications, medicine.anatomical_structure, Modeling and Simulation, Infection, cell cycle regulation, Research Article
Abstract: Methylation of specific DNA sequences is ubiquitous in bacteria and has known roles in immunity and regulation of cellular processes, such as the cell cycle. Here, we explored DNA methylation in bacteria of the genus Ensifer, including its potential role in regulating terminal differentiation during nitrogen-fixing symbiosis with legumes. Using single-molecule real-time sequencing, six genome-wide methylated motifs were identified across four Ensifer strains, five of which were strain-specific. Only the GANTC motif, recognized by the cell cycle-regulated CcrM methyltransferase, was methylated in all strains. In actively dividing cell cultures, methylation of GANTC motifs increased progressively from the ori to ter regions in each replicon, in agreement with a cell cycle-dependent regulation of CcrM. In contrast, there was near full genome-wide GANTC methylation in the early stage of symbiotic differentiation. This was followed by a moderate decrease in the overall extent of methylation and a progressive decrease in chromosomal GANTC methylation from the ori to ter regions in later stages of differentiation. Based on these observations, we suggest that CcrM activity is dysregulated and constitutive during terminal differentiation, which we hypothesize is a driving factor for endoreduplication of terminally differentiated bacteroids. IMPORTANCE Nitrogen fixation by rhizobia in symbiosis with legumes is economically and ecologically important. The symbiosis can involve a complex bacterial transformation—terminal differentiation—that includes major shifts in the transcriptome and cell cycle. Epigenetic regulation is an important regulatory mechanism in diverse bacteria; however, the roles of DNA methylation in rhizobia and symbiotic nitrogen fixation have been poorly investigated. We show that aside from cell cycle regulation, DNA methyltransferases are unlikely to have conserved roles in the biology of bacteria of the genus Ensifer. However, we present evidence consistent with an interpretation that the cell cycle methyltransferase CcrM is dysregulated during symbiosis, which we hypothesize may be a key factor driving the cell cycle switch in terminal differentiation required for effective symbioses.
Published: 2022

31. Tracking N-terminal protein processing from the Golgi to the chromatophore of a rhizarian amoeba

Author: Thierry Meinnel, Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Maturation des proteines, destinée cellulaire et thérapeutique (PROMTI), Département Biologie des Génomes (DBG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Fondation ARC (ARCPJA32020060002137), ANR-17-CAPS-0001,KatNat,Elucider les fonctions multifacettes des protéines acétyl transferase en réponse au stress et dans la régulation métabolique(2017), ANR-20-CE92-0040,CANMORE,Impact des modifications cotranslationnelles N-terminales plastidiales lors de la réponse au stress(2020), and ANR-11-IDEX-0003,IPS,Idex Paris-Saclay(2011)
Subjects: Physiology, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Golgi Apparatus, Plant Science, Chromatophores, Amoeba, Symbiosis
Abstract: International audience; Mass spectrometry analysis of protein processing in a photosynthetic rhizarian amoeba, Paulinella chromatophora, suggests a major trafficking route from the cytosol to the chromatophore via the Golgi.
Published: 2022

32. N-terminal modifications, the associated processing machinery, and their evolution in plastid-containing organisms

Author: Carmela Giglione, Thierry Meinnel, Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Maturation des proteines, destinée cellulaire et thérapeutique (PROMTI), Département Biologie des Génomes (DBG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Fondation ARC (ARCPJA32020060002137), ANR-20-CE92-0040,CANMORE,Impact des modifications cotranslationnelles N-terminales plastidiales lors de la réponse au stress(2020), ANR-20-CE44-0013,DynaMYT,Une combinaison de nouveaux outils chimiques pour élucider la dynamique du Myristome(2020), and ANR-11-IDEX-0003,IPS,Idex Paris-Saclay(2011)
Subjects: proteolysis, aminopeptidase, Physiology, formylation, oxidation, Ribulose-Bisphosphate Carboxylase, myristoylation, Plant Science, deformylation, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, Actins, Evolution, Molecular, arginylation, Plastids, methylation, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], Symbiosis, plastid, Phylogeny, acetylation
Abstract: The N-terminus is a frequent site of protein modifications. Referring primarily to knowledge gained from land plants, here we review the modifications that change protein N-terminal residues and provide updated information about the associated machinery, including that in Archaeplastida. These N-terminal modifications include many proteolytic events as well as small group additions such as acylation or arginylation and oxidation. Compared with that of the mitochondrion, the plastid-dedicated N-terminal modification landscape is far more complex. In parallel, we extend this review to plastid-containing Chromalveolata including Stramenopiles, Apicomplexa, and Rhizaria. We report a well-conserved machinery, especially in the plastid. Consideration of the two most abundant proteins on Earth—Rubisco and actin—reveals the complexity of N-terminal modification processes. The progressive gene transfer from the plastid to the nuclear genome during evolution is exemplified by the N-terminus modification machinery, which appears to be one of the latest to have been transferred to the nuclear genome together with crucial major photosynthetic landmarks. This is evidenced by the greater number of plastid genes in Paulinellidae and red algae, the most recent and fossil recipients of primary endosymbiosis.
Published: 2022

33. First tests of Li$_2$W$_4$ bolometric detectors using MMC sensors for the detection of CE$\nu$NS

Author: B. Mauri, M. Loidl, C. Nones, M. Rodrigues, M. Vivier, Institut de Recherches sur les lois Fondamentales de l'Univers (IRFU), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Laboratoire d'Intégration des Systèmes et des Technologies (LIST (CEA)), Direction de Recherche Technologique (CEA) (DRT (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), ANR-10-LABX-0038,P2IO,Physics of the 2 infinities and the origins(2010), and ANR-11-IDEX-0003,IPS,Idex Paris-Saclay(2011)
Subjects: Neutrino physics, [PHYS]Physics [physics], Low temperature detectors, Coherent elastic neutrino-nucleus scattering, Cryogenics, Scintillating bolometers, General Materials Science, Magnetic metallic calorimeters, Condensed Matter Physics, Atomic and Molecular Physics, and Optics
Abstract: International audience; Coherent elastic neutrino-nucleus scattering (CE$\nu$NS), detected for the frst time more than 40 years after its prediction, represents an experimental challenge because of its signature: a single nuclear recoil with energy in the range of 10 eV to a few 10’s keV on average. One of the main features of CE$\nu$NS is its cross section, around two orders of magnitude higher compared with the inverse $\beta$ decay. BASKET (Bolometers At Sub keV Energy Threshold) project aims at investigating cryogenic calorimeters for the CE$\nu$NS detection, able to maintain the background level below the expected signature while being operated in above ground conditions in close vicinity to a nuclear reactor. The main requirements for such detectors are a low enough energy threshold of O(10 eV), and a fast signal rise time in the range of 0.1–1 ms to achieve good timing resolution and hence good mitigation of pile-up events. In this article, we report on the frst tests of a prototype detector coupling a Li$_$2WO$_4$ crystal to a magnetic metallic calorimeter (MMC) thermal sensor
Published: 2022

34. A Coq Formalization of Lebesgue Integration of Nonnegative Functions

Author: François Clément, Vincent Martin, Sylvie Boldo, Micaela Mayero, Florian Faissole, Formally Verified Programs, Certified Tools and Numerical Computations (TOCCATA), Inria Saclay - Ile de France, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire Méthodes Formelles (LMF), Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Ecole Normale Supérieure Paris-Saclay (ENS Paris Saclay)-CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Ecole Normale Supérieure Paris-Saclay (ENS Paris Saclay), Simulation for the Environment: Reliable and Efficient Numerical Algorithms (SERENA), Inria de Paris, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Centre d'Enseignement et de Recherche en Mathématiques et Calcul Scientifique (CERMICS), École des Ponts ParisTech (ENPC), Laboratoire de Mathématiques Appliquées de Compiègne (LMAC), Université de Technologie de Compiègne (UTC), Laboratoire d'Informatique de Paris-Nord (LIPN), Centre National de la Recherche Scientifique (CNRS)-Université Sorbonne Paris Nord, This work was partly supported by the Paris Île-de-France Region (DIM RFSI MILC). This work was partly supported by Labex DigiCosme (project ANR-11-LABEX-0045-DIGICOSME) operated by ANR as part of the program 'Investissement d’Avenir' Idex Paris-Saclay (ANR-11-IDEX-0003-02). This work was partly supported by the European Research Council (ERC) under the EuropeanUnion’s Horizon 2020 Research and Innovation Programme – Grant Agreement n◦810367., ANR-11-LABX-0045,DIGICOSME,Mondes numériques: Données, programmes et architectures distribués(2011), ANR-11-IDEX-0003,IPS,Idex Paris-Saclay(2011), and European Project: 810367,EMC2(2019)
Subjects: FOS: Computer and information sciences, Computer Science - Logic in Computer Science, Correctness, Measurable function, Lebesgue integration, 0102 computer and information sciences, 02 engineering and technology, [MATH.MATH-CA]Mathematics [math]/Classical Analysis and ODEs [math.CA], Mathematical proof, [MATH.MATH-FA]Mathematics [math]/Functional Analysis [math.FA], 01 natural sciences, Formal proof, symbols.namesake, Artificial Intelligence, formal proof, FOS: Mathematics, 0202 electrical engineering, electronic engineering, information engineering, Coq, Mathematics, Lemma (mathematics), Real analysis, [INFO.INFO-LO]Computer Science [cs]/Logic in Computer Science [cs.LO], 020207 software engineering, Logic in Computer Science (cs.LO), Functional Analysis (math.FA), Algebra, Mathematics - Functional Analysis, measure theory, Computational Theory and Mathematics, 010201 computation theory & mathematics, Simple function, symbols, Software
Abstract: Integration, just as much as differentiation, is a fundamental calculus tool that is widely used in many scientific domains. Formalizing the mathematical concept of integration and the associated results in a formal proof assistant helps in providing the highest confidence on the correctness of numerical programs involving the use of integration, directly or indirectly. By its capability to extend the (Riemann) integral to a wide class of irregular functions, and to functions defined on more general spaces than the real line, the Lebesgue integral is perfectly suited for use in mathematical fields such as probability theory, numerical mathematics, and real analysis. In this article, we present the Coq formalization of $$\sigma $$ -algebras, measures, simple functions, and integration of nonnegative measurable functions, up to the full formal proofs of the Beppo Levi (monotone convergence) theorem and Fatou’s lemma. More than a plain formalization of the known literature, we present several design choices made to balance the harmony between mathematical readability and usability of Coq theorems. These results are a first milestone toward the formalization of $$L^p$$ spaces such as Banach spaces.
Published: 2022

35. Combining IR and X‐ray microtomography data sets: Application to Itokawa particles and to Paris meteorite

Author: Akira Tsuchiyama, David Troadec, Tomoki Nakamura, Rosario Brunetto, Zahia Djouadi, Christophe Sandt, Anne Cécile Buellet, Alessandra Rotundi, Donia Baklouti, Ferenc Borondics, Alice Aléon-Toppani, Andrew King, Stefano Rubino, Z. Dionnet, Institut d'astrophysique spatiale (IAS), Université Paris-Sud - Paris 11 (UP11)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National d’Études Spatiales [Paris] (CNES), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Centre National d’Études Spatiales [Paris] (CNES), Laboratoire de Physiogénomique / NeuroTranscriptomes et Paléogénétique (LPG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Synchrotron SOLEIL (SSOLEIL), Centre National de la Recherche Scientifique (CNRS), Tohoku University [Sendai], Istituto di Astrofisica e Planetologia Spaziali - INAF (IAPS), Istituto Nazionale di Astrofisica (INAF), SMIS Beamline, Synchrotron SOLEIL, Institut d’Électronique, de Microélectronique et de Nanotechnologie - UMR 8520 (IEMN), Centrale Lille-Institut supérieur de l'électronique et du numérique (ISEN)-Université de Valenciennes et du Hainaut-Cambrésis (UVHC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université Polytechnique Hauts-de-France (UPHF), Centrale de Micro Nano Fabrication - IEMN (CMNF - IEMN), Centrale Lille-Institut supérieur de l'électronique et du numérique (ISEN)-Université de Valenciennes et du Hainaut-Cambrésis (UVHC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université Polytechnique Hauts-de-France (UPHF)-Centrale Lille-Institut supérieur de l'électronique et du numérique (ISEN)-Université de Valenciennes et du Hainaut-Cambrésis (UVHC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université Polytechnique Hauts-de-France (UPHF), Division of Earth and Planetary Sciences [Kyoto], Kyoto University, Centre National d’Etudes Spatiales, Agence Nationale de la Recherche, This work is supported by the 'IDI 2015' project funded by the IDEX Paris-Saclay (Grant ANR-11-IDEX- 0003-02). The FT-IR microspectroscopy activities are supported by grants from Région Ile-de-France (DIM-ACAV) and SOLEIL. This work has been funded by the Centre National d’Etudes Spatiales (CNES-France, Hayabusa2 mission) and by the ANR project CLASSY (Grant ANR-17-CE31-0004-02) of the French Agence Nationale de la Recherche. This work was partly supported by the French RENATECH network. We wish to thank the Italian Space Agency (ASI, Italy) contract no. I/024/12/2 and MIUR, contracts PNRA16-00029 and PRIN2015-20158W4JZ7. We are grateful to the JAXA Curator for allocating the Hayabusa particles. We thank T. Yada and L. Bonal for useful discussion, B. Zanda for providing the Paris meteorite sample, and the ANATOMIX team (SOLEIL) for their help with Avizo., Renatech Network, ANR-11-IDEX-0003,IPS,Idex Paris-Saclay(2011), ANR-17-CE31-0004,CLASSY,Composition des surfaces du Système Solaire de bas albédo(2017), Université Paris-Sud - Paris 11 (UP11)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Centrale de Micro Nano Fabrication - IEMN (CMNF-IEMN), and Kyoto University [Kyoto]
Subjects: [SPI]Engineering Sciences [physics], Geophysics, X-ray microtomography, Materials science, Meteorite, Space and Planetary Science, 0103 physical sciences, Mineralogy, 010502 geochemistry & geophysics, 010303 astronomy & astrophysics, 01 natural sciences, 0105 earth and related environmental sciences
Abstract: International audience; In the near future, a new generation of sample return missions (Hayabusa2, OSIRIS-REx, MMX, etc.) will collect samples from small solar system bodies. To maximize the scientific outcome of laboratory studies and minimize the loss of precious extraterrestrial samples, an analytical sequence from less destructive to more destructive techniques needs to be established. In this work, we present a combined X-ray and IR microtomography applied to five Itokawa particles and one fragment of the primitive carbonaceous chondrite Paris. We show that this analytical approach is able to provide a 3-D physical and chemical characterization of individual extraterrestrial particles, using the measurement of their 3-D structure and porosity, and the detection of mineral and organic phases, and their spatial co-localization in 3-D. We propose these techniques as an efficient first step in a multitechnique analytical sequence on microscopic samples collected by space missions.
Published: 2020

36. Substrate Specificity of OXA-48 after β5−β6 Loop Replacement

Author: Agustin Zavala, Rémy A. Bonnin, Pascal Retailleau, Thierry Naas, Oliver Beckstein, Bogdan I. Iorga, Laura Dabos, Structure, Dynamique, Fonction Et Expression Des Beta-Lactamases À Large Spectre, Université Paris-Sud - Paris 11 - Faculté de médecine (UP11 UFR Médecine), Université Paris-Sud - Paris 11 (UP11)-Université Paris-Sud - Paris 11 (UP11)-Centre National de Référence de la Résistance aux Antibiotiques (CNR), Centre Hospitalier Régional Universitaire de Besançon (CHRU Besançon)-Centre Hospitalier Régional Universitaire de Besançon (CHRU Besançon), Institut de Chimie des Substances Naturelles (ICSN), Institut de Chimie du CNRS (INC)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Department of Physics, Arizona State University (ASU), Arizona State University [Tempe] (ASU), We acknowledge SOLEIL for provision of synchrotron radiation facilities (proposal ID BAG20170782) in using PROXIMA beamlines. This work has benefited from the platform and expertise of the Macromolecular Interactions Measurements Platform of I2BC and from the I2BC crystallization platform, supported by FRISBI ANR-10-INSB-05-01. This work was supported by the Assistance Publique − Hôpitaux de Paris (AP-HP), the University Paris-Sud, the Laboratory of Excellence in Research on Medication and Innovative Therapeutics (LERMIT) supported by a grant from the French National Research Agency [ANR-10-LABX-33], by the Joint Programming Initiative on Antimicrobial Resistance (JPIAMR) DesInMBL [ANR-14-JAMR-002], and by DIM Malinf, Ile de France, for L.D.’s Ph.D. fellowship., ANR-11-IDEX-0003,IPS,Idex Paris-Saclay(2011), ANR-14-JAMR-0002,DesInMBL,Structure-guided design of pan inhibitors of metallo-ß-lactamases(2014), and ANR-10-INBS-0005,FRISBI,Infrastructure Française pour la Biologie Structurale Intégrée(2010)
Subjects: 0301 basic medicine, Molecular model, Stereochemistry, 030106 microbiology, Crystallography, X-Ray, β5−β6 loop, beta-Lactamases, Substrate Specificity, Carbapenemase, 03 medical and health sciences, Hydrolysis, polycyclic compounds, Enzyme kinetics, expanded-spectrum cephalosporins, chemistry.chemical_classification, oxacillinases, Substrate (chemistry), biochemical phenomena, metabolism, and nutrition, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Cephalosporins, Amino acid, Loop (topology), Kinetics, 030104 developmental biology, Infectious Diseases, Enzyme, Carbapenems, chemistry, bacteria, β5-β6 loop, Function (biology)
Abstract: International audience; OXA-48 carbapenemase has rapidly spread in many countries worldwide with several OXA-48-variants being described, differing by a few amino acid (AA) substitutions or deletions, mostly in the β5-β6 loop. While single AA substitutions have only a minor impact on OXA-48 hydrolytic profiles, others with 4 AA deletions result in loss of carbapenem hydrolysis and gain of expanded-spectrum cephalosporin (ESC) hydrolysis. We have replaced the β5-β6 loop of OXA-48 with that of OXA-18, a clavulanic-acid inhibited oxacillinase capable of hydrolyzing ESCs but not carbapenems. The hybrid enzyme OXA-48Loop18 was able to hydrolyze ESCs and carbapenems (although with a lower kcat), even though the β5-β6 loop was longer and its sequence quite different from that of OXA-48. The kinetic parameters of OXA-48Loop18 were in agreement with the MIC values. X-ray crystallography and molecular modeling suggest that the conformation of the grafted loop allows the binding of bulkier substrates, unlike that of the native loop, expanding the hydrolytic profile. This seems to be due not only to differences in AA sequence, but also to the backbone conformation the loop can adopt. Finally, our results provide further experimental evidence for the role of the β5-β6 loop in substrate selectivity of OXA-48-like enzymes and additional details on the structure-function relationship of β-lactamases, demonstrating how localized changes in these proteins can alter or expand their function, highlighting their plasticity.
Published: 2020

37. Demand response versus storage flexibility in energy: multi-objective programming considerations

Author: Hasnaa Zidani, Claudia Sagastizábal, Ana Paula Chorobura, Wim van Ackooij, Électricité de France. Division Recherches et développement. Département OSIRIS, Optimisation et commande (OC), Unité de Mathématiques Appliquées (UMA), École Nationale Supérieure de Techniques Avancées (ENSTA Paris)-École Nationale Supérieure de Techniques Avancées (ENSTA Paris), Institute of Mathematics, Statistics, and Scientific Computing, State University of Campinas, ANR: IDEX PARIS SACLAY,ANR-11-IDEX-0003-02 IDEX Paris-Saclay, ANR: PGMO-iCODE,Program PGMO-iCODE, and ANR-11-IDEX-0003,IPS,Idex Paris-Saclay(2011)
Subjects: Flexibility (engineering), 021103 operations research, Control and Optimization, Energy management, Applied Mathematics, Objective programming, 0211 other engineering and technologies, 02 engineering and technology, Management Science and Operations Research, 7. Clean energy, 01 natural sciences, [SPI.AUTO]Engineering Sciences [physics]/Automatic, Reliability engineering, 010101 applied mathematics, Demand response, [MATH.MATH-OC]Mathematics [math]/Optimization and Control [math.OC], 0101 mathematics, ComputingMilieux_MISCELLANEOUS, [MATH.MATH-NA]Mathematics [math]/Numerical Analysis [math.NA], Energy (signal processing), Mathematics
Abstract: Intermittent sources of energy represent a challenge for electrical networks, particularly regarding demand satisfaction at peak times. Energy management tools such as load shaving or stora...
Published: 2020

38. An energy-based model to analyze growth data of earthworms exposed to two fungicides

Author: Isabelle Lamy, Céline Pelosi, Sylvie Nélieu, Sylvain Bart, Alexandre R.R. Pery, Ecologie fonctionnelle et écotoxicologie des agroécosystèmes (ECOSYS), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Environnement Méditerranéen et Modélisation des Agro-Hydrosystèmes (EMMAH), Avignon Université (AU)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), 'IDI 2015' project funded by the IDEX Paris-Saclay ANR-11-IDEX-0003-02, and ANR-11-IDEX-0003,IPS,Idex Paris-Saclay(2011)
Subjects: Toxicokinetic-toxicodynamicmodeling, Eisenia fetida, Toxicodynamics, Health, Toxicology and Mutagenesis, Growth, [SDV.SA.SDS]Life Sciences [q-bio]/Agricultural sciences/Soil study, 010501 environmental sciences, Ecotoxicology, Risk Assessment, 01 natural sciences, chemistry.chemical_compound, Animal science, biology.animal, Toxicity Tests, Animals, Soil Pollutants, Environmental Chemistry, Lumbricidae, Epoxiconazole, Oligochaeta, Pesticides, 0105 earth and related environmental sciences, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, biology, Hatching, Earthworm, DEBtox, General Medicine, Triazoles, biology.organism_classification, Pollution, Fungicides, Industrial, Fungicide, chemistry, Epoxy Compounds, Copper
Abstract: International audience; The pesticide risk assessment for earthworms is currently performed using standardized tests, the model species Eisenia fetida, and the analyses of the data obtained are performed with ad hoc statistical tools. We assessed the impact of two fungicides on the entire growth pattern of the earthworm species Aporrectodea caliginosa, which is highly representative of agricultural fields. Individuals of three different ages (from hatching to 56 days old) were exposed to Cuprafor micro(R) (copper oxychloride) and Swing(R) Gold (dimoxystrobin and epoxiconazole). Data were analyzed with an energy-based toxicodynamic model coupled with a toxicokinetic model. The copper fungicide caused a drastic growth inhibition once the no effect concentration (NEC), estimated at 65 mg kg(-1) of copper, was exceeded. The Swing(R) Gold negatively affected the growth with NEC values estimated at 0.387 mg kg(-1) and 0.128 mg kg(-1) for the dimoxystrobin and the epoxiconazole in this fungicide formulation, respectively. The time-profile of the effects on A. caliginosa individuals was fully accounted for by the model, whatever their age of exposure. Furthermore, toxicity data analyses, supported by measurements of fungicide concentrations in earthworm at the end of the experiment, allowed bettering understanding of the mechanisms of action of the fungicides towards earthworm growth.
Published: 2019

39. A Framework for Visualization and Analysis of Agronomic Field Trials from On‐Farm Research Networks

Author: David Makowski, Fernando E. Miguez, Peter M. Kyveryga, Anabelle Laurent, Agronomie (Agronomie), Institut National de la Recherche Agronomique (INRA)-Institut National Agronomique Paris-Grignon (INA P-G), Iowa Soybean Association, Iowa State University (ISU), Iowa Soybean Association STIMUL (Scenarios towards integrating multiscale land use tools) flagship project as part as part of the 'Investments d'Avenir' Programme (LabEx BASC) ANR-11-LABX-0034Institut Carnot Plant2Pro (project L-i-cite) Chateaubriand Fellowship of the Office for Science & Technology of the Embassy of France in the United States Plant Sciences Institute at Iowa State University Iowa Soybean Research Center at Iowa State University, and ANR-11-IDEX-0003,IPS,Idex Paris-Saclay(2011)
Subjects: 2. Zero hunger, 0106 biological sciences, Computer science, 04 agricultural and veterinary sciences, Agricultural engineering, 15. Life on land, 01 natural sciences, Field (geography), Visualization, Agronomy, [SDE]Environmental Sciences, Computer software, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Crop management, Agronomy and Crop Science, 010606 plant biology & botany
Abstract: An on-farm research network is an organization of farmers that conducts agronomic experiments under local conditions. It is common that an elementary statistical analysis be conducted for individual studies. However, there is unexplored potential in detecting yield response variability patterns for better decision making. We developed a data-analytics framework and web-application program that allows users to analyze multiple studies that use a common protocol and can identify the conditions where an imposed treatment may or may not be effective. The development of this data-analytics framework is needed to improve predictions at the farm level that can lead to more cost-effective, sustainable and environmentally sound agricultural production. Data visualization is an important part of data-analytics. In this paper, we have developed and tested a Bayesian hierarchical model that can be used to assess the general agro-nomic performance of different management practices. Decision making related to new management practices should be based on the complete evidence, local conditions and economic considerations. The web-application includes dynamic data visualization features to enhance communication and sharing of information with the goal to reach a broader audience. core Ideas • We develop a data-analytics framework and web-application for on-farm research trials. • A Bayesian hierarchical model quantifies the uncertainty in yield response. • The model helps assess alternative practices, products, and technologies among trial locations. • The framework provides a reactive break-even economic analysis of alternative management practices.
Published: 2019

40. A vacuolar hexose transport is required for xylem development in the inflorescence stem

Author: Emilie Aubry, Beate Hoffmann, Françoise Vilaine, Françoise Gilard, Patrick A W Klemens, Florence Guérard, Bertrand Gakière, H Ekkehard Neuhaus, Catherine Bellini, Sylvie Dinant, Rozenn Le Hir, Institut Jean-Pierre Bourgin (IJPB), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Technische Universität Kaiserslautern (TU Kaiserslautern), Department of Plant Physiology, UPSC, Umeå University, ANR-17-EURE-0007,SPS-GSR,Ecole Universitaire de Recherche de Sciences des Plantes de Paris-Saclay(2017), and ANR-11-IDEX-0003,IPS,Idex Paris-Saclay(2011)
Subjects: Genotype, Physiology, Regular Issue Content, fungi, Arabidopsis, food and beverages, Genetic Variation, Biological Transport, Plant Science, Xylem, Mutation, Vacuoles, Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Inflorescence, Hexoses
Abstract: In Angiosperms, the development of the vascular system is controlled by a complex network of transcription factors. However, how nutrient availability in the vascular cells affects their development remains to be addressed. At the cellular level, cytosolic sugar availability is regulated mainly by sugar exchanges at the tonoplast through active and/or facilitated transport. In Arabidopsis (Arabidopsis thaliana), among the genes encoding tonoplastic transporters, SUGAR WILL EVENTUALLY BE EXPORTED TRANSPORTER 16 (SWEET16) and SWEET17 expression has been previously detected in the vascular system. Here, using a reverse genetics approach, we propose that sugar exchanges at the tonoplast, regulated by SWEET16, are important for xylem cell division as revealed in particular by the decreased number of xylem cells in the swt16 mutant and the accumulation of SWEET16 at the procambium–xylem boundary. In addition, we demonstrate that transport of hexoses mediated by SWEET16 and/or SWEET17 is required to sustain the formation of the xylem secondary cell wall. This result is in line with a defect in the xylem cell wall composition as measured by Fourier-transformed infrared spectroscopy in the swt16swt17 double mutant and by upregulation of several genes involved in secondary cell wall synthesis. Our work therefore supports a model in which xylem development partially depends on the exchange of hexoses at the tonoplast of xylem-forming cells.
Published: 2021

41. Identification of Small Molecules Inhibiting Cardiomyocyte Necrosis and Apoptosis by Autophagy Induction and Metabolism Reprogramming

Author: Dawei Liu, Félix Peyre, Yahir Alberto Loissell-Baltazar, Delphine Courilleau, Sandra Lacas-Gervais, Valérie Nicolas, Eric Jacquet, Svetlana Dokudovskaya, Frédéric Taran, Jean-Christophe Cintrat, Catherine Brenner, JACQUET, ERIC, Idex Paris-Saclay - - IPS2011 - ANR-11-IDEX-0003 - IDEX - VALID, Research Laboratory on Drugs and Therapeutic Innovation - - LERMIT2010 - ANR-10-LABX-0033 - LABX - VALID, Lanzhou University, Aspects métaboliques et systémiques de l'oncogénèse pour de nouvelles approches thérapeutiques (METSY), Institut Gustave Roussy (IGR)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Ingénierie et Plateformes au Service de l'Innovation Thérapeutique (IPSIT), Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), CCMA - Centre Commun de Microscopie Appliquée, Université Côte d'Azur (UCA), Institut de Chimie des Substances Naturelles (ICSN), Institut de Chimie du CNRS (INC)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Service de Chimie Bio-Organique et de Marquage (SCBM), Médicaments et Technologies pour la Santé (MTS), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ANR-11-IDEX-0003,IPS,Idex Paris-Saclay(2011), and ANR-10-LABX-0033,LERMIT,Research Laboratory on Drugs and Therapeutic Innovation(2010)
Subjects: QH301-705.5, screening, cardiotoxicity, Apoptosis, General Medicine, Hydrogen Peroxide, [SDV.MHEP.CSC] Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, Rats, Necrosis, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, [SDV.SP.PHARMA] Life Sciences [q-bio]/Pharmaceutical sciences/Pharmacology, cardioprotection, [SDV.SP.PHARMA]Life Sciences [q-bio]/Pharmaceutical sciences/Pharmacology, Autophagy, mitochondrion, Animals, Humans, apoptosis, autophagy, Myocytes, Cardiac, Biology (General)
Abstract: International audience; Improvement of anticancer treatments is associated with increased survival of cancer patients at risk of cardiac disease. Therefore, there is an urgent need for new therapeutic molecules capable of preventing acute and long-term cardiotoxicity. Here, using commercial and home-made chemolibraries, we performed a robust phenotypic high-throughput screening in rat cardiomyoblast cell line H9c2, searching for small molecules capable of inhibiting cell death. A screen of 1600 compounds identified six molecules effective in preventing necrosis and apoptosis induced by H$_2$O$_2$ and camptothecin in H9c2 cells and in rat neonatal ventricular myocytes. In cells treated with these molecules, we systematically evaluated the expression of BCL-2 family members, autophagy progression, mitochondrial network structure, regulation of mitochondrial fusion/fission, reactive oxygen species, and ATP production. We found that these compounds affect autophagy induction to prevent cardiac cell death and can be promising cardioprotective drugs during chemotherapy.
Published: 2021

42. Collective Effects in Ionic Liquid [emim][Tf2N] and Ionic Paramagnetic Nitrate Solutions without Long-Range Structuring

Author: Eni Kume, Nicolas Martin, Peter Dunne, Patrick Baroni, Laurence Noirez, Laboratoire Léon Brillouin (LLB - UMR 12), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), LLB - Nouvelles frontières dans les matériaux quantiques (NFMQ), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Institut de Physique et Chimie des Matériaux de Strasbourg (IPCMS), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Matériaux et Nanosciences Grand-Est (MNGE), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Réseau nanophotonique et optique, Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), ANR-11-IDEX-0003,IPS,Idex Paris-Saclay(2011), European Project: 766007,MAMI, NOIREZ, Laurence, Idex Paris-Saclay - - IPS2011 - ANR-11-IDEX-0003 - IDEX - VALID, and Magnetics and Microhydrodynamics - from guided transport to delivery - MAMI - 766007 - INCOMING
Subjects: paramagnetic liquids, [PHYS]Physics [physics], ionic liquids, mechanical measurements, shear elasticity, neutron scattering, Organic Chemistry, Pharmaceutical Science, [PHYS.COND.CM-MS] Physics [physics]/Condensed Matter [cond-mat]/Materials Science [cond-mat.mtrl-sci], [PHYS] Physics [physics], Analytical Chemistry, Chemistry (miscellaneous), Drug Discovery, [PHYS.COND.CM-MS]Physics [physics]/Condensed Matter [cond-mat]/Materials Science [cond-mat.mtrl-sci], Molecular Medicine, Physical and Theoretical Chemistry
Abstract: International audience; Mesoscopic shear elasticity has been revealed in ordinary liquids both experimentally by reinforcing the liquid/surface interfacial energy and theoretically by nonextensive models. The elastic effects are here examined in the frame of small molecules with strong electrostatic interactions such as room temperature ionic liquids [emim][Tf2N] and nitrate solutions exhibiting paramagnetic properties. We first show that these charged fluids also exhibit a nonzero lowfrequency shear elasticity at the submillimeter scale, highlighting their resistance to shear stress. A neutron scattering study completes the dynamic mechanical analysis of the paramagnetic nitrate solution, evidencing that the magnetic properties do not induce the formation of a structure in the solution. We conclude that the elastic correlations contained in liquids usually considered as viscous away from any phase transition contribute in an effective way to collective effects under external stress or mechanical and magnetic fields.
Published: 2022

43. New Features of P3$\delta$ software: Partial Pole Placement via Delay Action

Author: Silviu-Iulian Niculescu, Islam Boussaada, Max Perraudin, Adrien Leclerc, Guilherme Mazanti, Jayvir Raj, Institut Polytechnique des Sciences Avancées (IPSA), Dynamical Interconnected Systems in COmplex Environments (DISCO), Inria Saclay - Ile de France, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire des signaux et systèmes (L2S), CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), This work is partially supported by a public grant overseen by the French National Research Agency (ANR) as part of the 'Investissement d’Avenir' program, through the iCODE project funded by the IDEX Paris-Saclay, ANR-11-IDEX-0003-02. The authors also acknowledge the support of Institut Polytechnique des Sciences Avancées (IPSA)., and ANR-11-IDEX-0003,IPS,Idex Paris-Saclay(2011)
Subjects: 0209 industrial biotechnology, Time-delay systems, Controller design, Computer science, Stability (learning theory), 010103 numerical & computational mathematics, 02 engineering and technology, 01 natural sciences, Online software, [SPI.AUTO]Engineering Sciences [physics]/Automatic, Set (abstract data type), 020901 industrial engineering & automation, Software, Control theory, Full state feedback, GUI, 0101 mathematics, Mathematics - Optimization and Control, Parametric statistics, computer.programming_language, Delay, business.industry, Python (programming language), Stabilization, Control and Systems Engineering, Control system, [MATH.MATH-OC]Mathematics [math]/Optimization and Control [math.OC], User interface, business, computer, Stability, Python toolbox
Abstract: This paper presents the software Partial Pole Placement via Delay Action, or P3$\delta$ for short. P3$\delta$ is a Python software with a friendly user interface for the design of parametric stabilizing feedback laws with time-delays, thanks to two properties of the distribution of quasipolynomials' zeros, called multiplicity-induced-dominancy and coexisting real roots-induced-dominancy. After recalling recent theoretical results on these properties and their use for the feedback stabilization of control systems operating under time delays, the paper presents the main features of the current version of P3$\delta$. We detail, in particular, the assignable admissible region (the set of allowable dominant roots and the corresponding delay), which helps the user in the choice of input information, allowing a reliable stabilizing delayed feedback. We also present the newly set online version of P3$\delta$., Comment: 16th IFAC Workshop on Time Delay Systems (IFAC TDS 2021). arXiv admin note: substantial text overlap with arXiv:2007.05809
Published: 2021

44. Functional–Structural Plant Modeling Highlights How Diversity in Leaf Dimensions and Tillering Capability Could Promote the Efficiency of Wheat Cultivar Mixtures

Author: Emmanuelle Blanc, Pierre Barbillon, Christian Fournier, Christophe Lecarpentier, Christophe Pradal, Jérôme Enjalbert, Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) (GQE-Le Moulon), AgroParisTech-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Mathématiques et Informatique Appliquées (MIA-Paris), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-AgroParisTech-Université Paris-Saclay, Écophysiologie des Plantes sous Stress environnementaux (LEPSE), Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Clermont Auvergne (UCA), Scientific Data Management (ZENITH), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), ANR-11-IDEX-0003,IPS,Idex Paris-Saclay(2011), ANR-20-PCPA-0006,MoBiDiv,Mobilizing and Breeding Intra and inter-specific crop Diversity for a systemic change towards pesticide-free agriculture(2020), Mathématiques et Informatique Appliquées (MIA Paris-Saclay), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Inria Sophia Antipolis - Méditerranée (CRISAM), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro
Subjects: 0106 biological sciences, Canopy, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, F08 - Systèmes et modes de culture, [SDV]Life Sciences [q-bio], Plant Science, Agricultural engineering, Performance de culture, 01 natural sciences, F50 - Anatomie et morphologie des plantes, SB1-1110, sensitivity analysis, Cultivar, functional traits, Original Research, Mathematics, 2. Zero hunger, competition for light, Tallage, U10 - Informatique, mathématiques et statistiques, 04 agricultural and veterinary sciences, tillering plasticity, Anatomie végétale, Diversification, Trait, Interception, Assembly rules, Triticum aestivum, Crop, aerial architecture, variety mixture, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Variété, Leaf area index, Morphologie végétale, Modélisation des cultures, Plant culture, 15. Life on land, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Cropping, 010606 plant biology & botany
Abstract: International audience; Increasing the cultivated diversity has been identified as a major leverage for the agroecological transition as it can help improve the resilience of low input cropping systems. For wheat, which is the most cultivated crop worldwide in terms of harvested area, the use of cultivar mixtures is spreading in several countries, but studies have seldom focused on establishing mixing rules based on plant architecture. Yet, the aerial architecture of plants and the overall canopy structure are critical for field performance as they greatly influence light interception, plant interactions and yield. The very high number of trait combinations in wheat mixtures makes it difficult to conduct experimentations on this issue, which is why a modeling approach appears to be an appropriate solution. In this study, we used WALTer, a functional structural plant model (FSPM), to simulate wheat cultivar mixtures and try to better understand how differences between cultivars in key traits of the aerial architecture influence mixture performance. We simulated balanced binary mixtures of cultivars differing for different critical plant traits: final height, leaf dimensions, leaf insertion angle and tillering capability. Our study highlights the impact of the leaf dimensions and the tillering capability on the performance of the simulated mixtures, which suggests that traits impacting the plants' leaf area index (LAI) have more influence on the performance of the stand than traits impacting the arrangement of the leaves. Our results show that the performance of mixtures is very variable depending on the values of the explored architectural traits. In particular, the best performances were achieved by mixing cultivars with different leaf dimensions and different tillering capability, which is in agreement with numerous studies linking the diversity of functional traits in plant communities to their productivity. However, some of the worst performances were also achieved by mixing varieties differing in their aerial architecture, which suggests that diversity is not a sufficient criterion to design efficient mixtures. Overall, these results highlight the importance of simulation-based explorations for establishing assembly rules to design efficient mixtures.
Published: 2021

45. Brachypodium distachyon UNICULME4 and LAXATUM-A are redundantly required for development

Author: Kevin Magne, Sylviane Daniel, Shengbin Liu, Richard Sibout, Pascal Ratet, Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité de recherche sur les Biopolymères, Interactions Assemblages (BIA), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), TRANSFORM Division (INRAE), S. Liu was supported by a 4-year Chinese scholarship council PhD 38 scholarship (CSC grant n° 201608510056)., ANR-14-CE19-0003,NOOT,Les gènes NOOT gardiens de l'dentité des nodosités symbiotiques et de l'abscission(2014), ANR-14-CE19-0012,BRAVO,Ontogénie des tissus vasculaires chez les graminées(2014), ANR-10-LABX-0040,SPS,Saclay Plant Sciences(2010), ANR-17-EURE-0007,SPS-GSR,Ecole Universitaire de Recherche de Sciences des Plantes de Paris-Saclay(2017), ANR-11-IDEX-0003,IPS,Idex Paris-Saclay(2011), and Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: 0106 biological sciences, TILLING, Genotype, Physiology, Plant Science, Genes, Plant, 01 natural sciences, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, 03 medical and health sciences, Abscission, Gene Expression Regulation, Plant, Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Inflorescence, Gene, Conserved Sequence, Research Articles, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, Oryza sativa, biology, Genetic Variation, food and beverages, biology.organism_classification, Reverse Genetics, Plant Leaves, Mutation, Seeds, [SDE]Environmental Sciences, Brachypodium, Brachypodium distachyon, Hordeum vulgare, 010606 plant biology & botany
Abstract: In cultivated grasses, tillering, leaf, and inflorescence architecture, as well as abscission ability, are major agronomical traits. In barley (Hordeum vulgare), maize (Zea mays), rice (Oryza sativa), and brachypodium (Brachypodium distachyon), NOOT-BOP-COCH-LIKE (NBCL) genes are essential regulators of vegetative and reproductive development. Grass species usually possess 2–4 NBCL copies and until now a single study in O. sativa showed that the disruption of all NBCL genes strongly altered O. sativa leaf development. To improve our understanding of the role of NBCL genes in grasses, we extended the study of the two NBCL paralogs BdUNICULME4 (CUL4) and BdLAXATUM-A (LAXA) in the nondomesticated grass B. distachyon. For this, we applied reversed genetics and generated original B. distachyon single and double nbcl mutants by clustered regularly interspaced short palindromic repeats – CRISPR associated protein 9 (CRISPR-Cas9) approaches and genetic crossing between nbcl targeting induced local lesions in genomes (TILLING) mutants. Through the study of original single laxa CRISPR–Cas9 null alleles, we validated functions previously proposed for LAXA in tillering, leaf patterning, inflorescence, and flower development and also unveiled roles for these genes in seed yield. Furthermore, the characterization of cul4laxa double mutants revealed essential functions for nbcl genes in B. distachyon development, especially in the regulation of tillering, stem cell elongation and secondary cell wall composition as well as for the transition toward the reproductive phase. Our results also highlight recurrent antagonist interactions between NBCLs occurring in multiple aspects of B. distachyon development.
Published: 2021

46. Avoidance of detrimental defense responses in beneficial plant–microbe interactions

Author: Pascal Ratet, Benjamin Gourion, Laboratoire des Interactions Plantes Microbes Environnement (LIPME), Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ANR-14-CE19-0003,NOOT,Les gènes NOOT gardiens de l'dentité des nodosités symbiotiques et de l'abscission(2014), ANR-10-LABX-0040,SPS,Saclay Plant Sciences(2010), ANR-17-EURE-0007,SPS-GSR,Ecole Universitaire de Recherche de Sciences des Plantes de Paris-Saclay(2017), ANR-11-IDEX-0003,IPS,Idex Paris-Saclay(2011), ANR-10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2010), ANR-17-CE20-0013,TrolesInfidels,Compromis dans les symbioses rhizobium-légumineuse, influence de l'immunité et des défenses sur la symbiose et vice versa(2017), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, [SDV]Life Sciences [q-bio], Biomedical Engineering, Bioengineering, Biology, 01 natural sciences, Crop, 03 medical and health sciences, Stress, Physiological, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 2. Zero hunger, Abiotic component, 0303 health sciences, Resistance (ecology), business.industry, fungi, Plant microbe, food and beverages, 15. Life on land, Plants, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, Biotechnology, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, business, 010606 plant biology & botany, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: International audience; In the environment microbes interact with plants and provide them with benefits that include protection against biotic and abiotic stresses as well as improved nutrition. However, plants are also exposed to parasites and pathogens. To manage appropriate responses, evolution has resulted in improved tolerance of plants to beneficial microbes while keeping the ability to recognize detrimental ones and to develop defense responses. Here we review the mechanisms involved in these interactions. We also discuss how the interactions might be handled to improve crop resistance to pathogens without losing the ability to establish beneficial interactions.
Published: 2021

47. From hidden shear-elasticity to opto-and thermo-elasticity in confined polymer melts and viscous liquids

Author: Noirez, Laurence, Kume, Eni, Baroni, Patrick, LLB - Nouvelles frontières dans les matériaux quantiques (NFMQ), Laboratoire Léon Brillouin (LLB - UMR 12), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay, Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay, ANR-11-IDEX-0003,IPS,Idex Paris-Saclay(2011), European Project: 766007,MAMI, NOIREZ, Laurence, Idex Paris-Saclay - - IPS2011 - ANR-11-IDEX-0003 - IDEX - VALID, Magnetics and Microhydrodynamics - from guided transport to delivery - MAMI - 766007 - INCOMING, Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)
Subjects: Condensed Matter::Soft Condensed Matter, Physics::Fluid Dynamics, [PHYS.COND.CM-SCM]Physics [physics]/Condensed Matter [cond-mat]/Soft Condensed Matter [cond-mat.soft], [PHYS.COND.CM-SCM] Physics [physics]/Condensed Matter [cond-mat]/Soft Condensed Matter [cond-mat.soft]
Abstract: From the newly identified low frequency liquid elasticity, it turns out the possibility to reveal novel dynamic properties of liquids at mesoscopic scale. We present two examples illustrating the impact of the mesoscopic liquid elasticity in optics and thermodynamics. We show strain induced optical effects and thermo-induced effects that occur in the liquid state and reveal the need to take into consideration the elastic character of fluids at small scale. The fluids are submitted to a low frequency (~ Hz) mechanical shear strain (external stress). We probe the dynamic response by two methods, either accessing instant optical response of the liquid phase of liquid crystals and or probing the thermal response upon mechanical deformation. It is shown that the isotropic phase of liquid crystals can exhibit a dynamic birefringence in the isotropic phase while ordinary liquids exhibit cold and cold thermal waves upon low frequency excitation.
Published: 2021

48. Highlighting Thermo-Elastic Effects in Confined Fluids

Author: Laurence Noirez, P. Baroni, Eni Kume, LLB - Nouvelles frontières dans les matériaux quantiques (NFMQ), Laboratoire Léon Brillouin (LLB - UMR 12), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay, ANR-11-IDEX-0003,IPS,Idex Paris-Saclay(2011), European Project: 766007,MAMI, and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)
Subjects: Shear elasticity, Materials science, Polymers and Plastics, liquid state, polymer melt, Organic chemistry, 02 engineering and technology, Low frequency, 01 natural sciences, Article, shear strain, Physics::Fluid Dynamics, adiabatic transformation, QD241-441, 0103 physical sciences, Thermal, Shear stress, Coupling (piping), thermo-elasticity, [PHYS.COND]Physics [physics]/Condensed Matter [cond-mat], 010306 general physics, Mesoscopic physics, Thermo elastic, General Chemistry, Mechanics, 021001 nanoscience & nanotechnology, Shear (sheet metal), Condensed Matter::Soft Condensed Matter, shear elasticity, glass former, 0210 nano-technology
Abstract: International audience; The recent identification of a finite shear elasticity in mesoscopic fluids has motivated the search of other solid-like properties of liquids. We present an innovative thermal approach of liquids. We identify a dynamic thermo-elastic mesoscopic behavior by building the thermal image produced by different liquids upon applying a low frequency mechanical shear field. We selected three fluids: a low molecular weight polybutylacrylate (PBuA), polypropyleneglycol (PPG), and glycerol. We demonstrate that a part of the energy of the shear strain is converted in cold and hot shear bands varying synchronously with the applied shear field. This thermodynamic change suggests a coupling to shear elastic modes in agreement with the low frequency shear elasticity theoretically foreseen and experimentally demonstrated.
Published: 2021

49. Azetidinimines as a novel series of non-covalent broad-spectrum inhibitors of β-lactamases with submicromolar activities against carbapenemases KPC-2 (class A), NDM-1 (class B) and OXA-48 (class D)

Author: Mohamed Benchekroun, Saoussen Oueslati, Sandrine Ventre, Kamsana Vijayakumar, Eddy Elisée, Laetitia A. Nguyen, Edithe Selwa, Robert H. Dodd, Linda Tlili, Alain Pruvost, Pascal Retailleau, Thierry Naas, Agustin Zavala, Bogdan I. Iorga, Agathe C. A. D'Hollander, Eugénie Romero, Cynthia Exilie, Kevin Cariou, Corinne Minard, Institut de Chimie des Substances Naturelles (ICSN), Institut de Chimie du CNRS (INC)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), AP-HP Hôpital Bicêtre (Le Kremlin-Bicêtre), Immunologie des maladies virales, auto-immunes, hématologiques et bactériennes (IMVA-HB), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Saclay, Médicaments et Technologies pour la Santé (MTS), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Ecologie et Evolution de la Résistance aux Antibiotiques / Ecology and Evolution of Antibiotics Resistance (EERA), Institut Pasteur [Paris] (IP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), This work was supported by the Laboratory of Excellence in Research on Medication and Innovative Therapeutics (LERMIT, grant ANR-10-LABX-33 under the program Investissements d’Avenir ANR-11-IDEX-0003-01), the FCS Campus Paris-Saclay pre-maturation program (project Inhibase), the SATT Paris-Saclay (project CARBAMAT), the JPIAMR transnational project DesInMBL (grant ANR-14-JAMR-0002) and the Région Ile-de-France (DIM Malinf). The authors also thank CNRS, AP-HP, Université Paris-Saclay, and ICSN, for financial support., ANR-10-LABX-0033,LERMIT,Research Laboratory on Drugs and Therapeutic Innovation(2010), ANR-11-IDEX-0003,IPS,Idex Paris-Saclay(2011), ANR-14-JAMR-0002,DesInMBL,Structure-guided design of pan inhibitors of metallo-ß-lactamases(2014), Institut Pasteur [Paris]-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Cariou, Kevin, Research Laboratory on Drugs and Therapeutic Innovation - - LERMIT2010 - ANR-10-LABX-0033 - LABX - VALID, Idex Paris-Saclay - - IPS2011 - ANR-11-IDEX-0003 - IDEX - VALID, and programmation conjointe européenne sur la résistance antimicrobienne - Structure-guided design of pan inhibitors of metallo-ß-lactamases - - DesInMBL2014 - ANR-14-JAMR-0002 - JPI AMR - VALID
Subjects: Imipenem, Non covalent, Antibiotics, [CHIM.THER]Chemical Sciences/Medicinal Chemistry, medicine.disease_cause, 01 natural sciences, Broad spectrum, Catalytic Domain, Drug Discovery, polycyclic compounds, OXA-48, chemistry.chemical_classification, 0303 health sciences, biology, Escherichia coli Proteins, General Medicine, Ynamides, Anti-Bacterial Agents, Molecular Docking Simulation, Microsomes, Liver, beta-Lactamase Inhibitors, medicine.drug, Gram-negative bacteria, Carbapenemase inhibitors, medicine.drug_class, Stereochemistry, Azetidinimines, [CHIM.THER] Chemical Sciences/Medicinal Chemistry, Microbial Sensitivity Tests, NDM-1, beta-Lactamases, Bacterial resistance, KPC-2, Cell Line, Inhibitory Concentration 50, Structure-Activity Relationship, 03 medical and health sciences, Antibiotic resistance, Gram-Negative Bacteria, medicine, Humans, Escherichia coli, Cell Proliferation, 030304 developmental biology, Pharmacology, Binding Sites, 010405 organic chemistry, Organic Chemistry, biochemical phenomena, metabolism, and nutrition, biology.organism_classification, 0104 chemical sciences, Enzyme, chemistry, Azetidines
Abstract: International audience; The occurrence of resistances in Gram negative bacteria is steadily increasing to reach extremely worrying levels and one of the main causes of resistance is the massive spread of very efficient β-lactamases which render most β-lactam antibiotics useless. Herein, we report the development of a series of imino-analogues of β-lactams (namely azetidinimines) as efficient non-covalent inhibitors of β-lactamases. Despite the structural and mechanistic differences between serine-β-lactamases KPC-2 and OXA-48 and metallo-β-lactamase NDM-1, all three enzymes can be inhibited at a submicromolar level by compound 7dfm, which can also repotentiate imipenem against a resistant strain of Escherichia coli expressing NDM-1. We show that 7dfm can efficiently inhibit not only the three main clinically-relevant carbapenemases of Ambler classes A (KPC-2), B (NDM-1) and D (OXA-48) with Ki’s below 0.3 μM, but also the cephalosporinase CMY-2 (class C, 86% inhibition at 10 μM). Our results pave the way for the development of a new structurally original family of non-covalent broad-spectrum inhibitors of β-lactamases.
Published: 2021

50. The evolutionary conserved proteins CEP90, FOPNL, and OFD1 recruit centriolar distal appendage proteins to initiate their assembly

Author: Pierrick Le Borgne, Logan Greibill, Marine Hélène Laporte, Michel Lemullois, Khaled Bouhouche, Mebarek Temagoult, Olivier Rosnet, Maeva Le Guennec, Laurent Lignières, Guillaume Chevreux, France Koll, Virginie Hamel, Paul Guichard, Anne-Marie Tassin, Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Université de Genève = University of Geneva (UNIGE), Centre de Recherche en Cancérologie de Marseille (CRCM), Aix Marseille Université (AMU)-Institut Paoli-Calmettes, Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut Jacques Monod (IJM (UMR_7592)), Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), The present work has benefited from Imagerie-Gif core facility supported by I’Agence Nationale de la Recherche (ANR-11-EQPX-0029/ Morphoscope, ANR-10-INBS-04/ FranceBioImaging, ANR-11-IDEX-0003-02/ Saclay Abstract In metazoa, cilia assembly is a cellular process that starts with centriole to basal body maturation, migration to the cell surface, and docking to the plasma membrane. Basal body docking involves the interaction of both the distal end of the basal body and the transition fibers/ distal appendages, with the plasma membrane. Mutations in numerous genes involved in basal body docking and transition zone assembly are associated with the most severe ciliopathies, highlighting the importance of these events in cilium biogenesis. In this context, the ciliate Paramecium has been widely used as a model system to study basal body and cilia assembly. However, despite the evolutionary conservation of cilia assembly events across phyla, whether the same molecular players are functionally conserved, is not fully known. Here, we demonstrated that CEP90, FOPNL, andOFD1areevolutionary conserved proteins crucial for ciliogenesis. Using ultrastructure expansion microscopy, we unveiled that these proteins localize at the distal end of both centrioles/basal bodies in Paramecium and mammaliancells. Moreover, we found that these proteins are recruited early during centriole duplication on the external surface of the procentriole. Functional analysis performed both in Paramecium andmammaliancells demonstrate the requirement of these proteins for distal appendage assembly andbasal body docking. Finally, we show that mammalian centrioles require another component, Moonraker (MNR), to recruit OFD1, FOPNL, and CEP90, which will then recruit the distal appendage proteins CEP83, CEP89, and CEP164. Altogether, we propose that this OFD1, FOPNL, and CEP90 functional module is required to determine in mammalian cells the future position of distal appendage proteins. PLOSBiology| https://doi.org/10.1371/journal.pbio.3001782 September 7, 2022 1/ 37PLOS BIOLOGY Theevolutionary conserved proteins CEP90, FOPNL andOFD1recruit centriolar distal appendage proteins Plant Sciences). This work has been founded by 'Basal body anchoring in ciliogenesis: structurefunction analysis: ANR-15-CE11-0002-01' to AMT. PLB was supported by PhD fellowships from Universite´ Paris-Saclay (https://www.paris-saclay. fr/). This work has been supported by the Fondation 'ARC pour la recherche sur le cancer' to PLB ARCDOC4202003000178 and by the Swiss National Science Foundation (SNSF) PP00P3_187198 and by the European research Council ERC ACCENT StG 715289 attributed to PG., ANR-11-EQPX-0029,MORPHOSCOPE 2,Imagerie et reconstruction multiéchelles de la morphogenèse. (Plateforme d'innovation technologique et méthodologique pour l'imagerie in vivo et la reconstruction des dynamiques multiéchelles de la morphogenèse)(2011), ANR-11-IDEX-0003,IPS,Idex Paris-Saclay(2011), and ANR-15-CE11-0002,ANCHOR,Ancrage des corps basaux pendant la ciliogenèse : analyse structure-fonction(2015)
Subjects: Mammals, Paramecium, General Immunology and Microbiology, [SDV]Life Sciences [q-bio], [SDV.BA]Life Sciences [q-bio]/Animal biology, General Neuroscience, Cell Membrane, Animals, Cilia, General Agricultural and Biological Sciences, General Biochemistry, Genetics and Molecular Biology, Centrioles, [SHS]Humanities and Social Sciences
Abstract: In metazoa, cilia assembly is a cellular process that starts with centriole to basal body maturation, migration to the cell surface, and docking to the plasma membrane. Basal body docking involves the interaction of both the distal end of the basal body and the transition fibers/distal appendages, with the plasma membrane. Mutations in numerous genes involved in basal body docking and transition zone assembly are associated with the most severe ciliopathies, highlighting the importance of these events in cilium biogenesis. In this context, the ciliate Paramecium has been widely used as a model system to study basal body and cilia assembly. However, despite the evolutionary conservation of cilia assembly events across phyla, whether the same molecular players are functionally conserved, is not fully known. Here, we demonstrated that CEP90, FOPNL, and OFD1 are evolutionary conserved proteins crucial for ciliogenesis. Using ultrastructure expansion microscopy, we unveiled that these proteins localize at the distal end of both centrioles/basal bodies in Paramecium and mammalian cells. Moreover, we found that these proteins are recruited early during centriole duplication on the external surface of the procentriole. Functional analysis performed both in Paramecium and mammalian cells demonstrate the requirement of these proteins for distal appendage assembly and basal body docking. Finally, we show that mammalian centrioles require another component, Moonraker (MNR), to recruit OFD1, FOPNL, and CEP90, which will then recruit the distal appendage proteins CEP83, CEP89, and CEP164. Altogether, we propose that this OFD1, FOPNL, and CEP90 functional module is required to determine in mammalian cells the future position of distal appendage proteins.
Published: 2022

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