Author: "École polytechnique (X)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)" - Searchworks@Jio Institute Digital Library Search Results

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733 results on '"École polytechnique (X)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)"'

1. Telomeres expand sphere of influence: emerging molecular impact of telomeres in non-telomeric functions

Author: Soujanya Vinayagamurthy, Sulochana Bagri, Jean-Louis Mergny, Shantanu Chowdhury, CSIR Institute of Genomics and Integrative Biology [New Delhi] (IGIB), Academy of Scientific and Innovative Research [Ghaziabad, India] (AcSIR), Partenaires INRAE, Laboratoire d'Optique et Biosciences (LOB), École polytechnique (X)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institute of Biophysics of the Czech Academy of Sciences (IBP / CAS), Czech Academy of Sciences [Prague] (CAS), and Mergny, Jean-Louis
Subjects: [SDV.GEN]Life Sciences [q-bio]/Genetics, G-quadruplex, aging, telomere signaling, [SDV.CAN]Life Sciences [q-bio]/Cancer, TRF2, [SDV.GEN] Life Sciences [q-bio]/Genetics, pluripotency, [SDV.CAN] Life Sciences [q-bio]/Cancer, gene-regulation, non-telomeric function, telomeric factors, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, Genetics, cancer, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology
Abstract: International audience; Although the impact of telomeres on physiology stands well established, a question remains: how do telomeres impact cellular functions at a molecular level? This is because current understanding limits the influence of telomeres to adjacent subtelomeric regions despite the wide-ranging impact of telomeres. Emerging work in two distinct aspects offers opportunities to bridge this gap. First, telomere-binding factors were found with non-telomeric functions. Second, locally induced DNA secondary structures called G-quadruplexes are notably abundant in telomeres, and gene regulatory regions genome wide. Many telomeric factors bind to G-quadruplexes for non-telomeric functions. Here we discuss a more general model of how telomeres impact the non-telomeric genome – through factors that associate at telomeres and genome wide – and influence cell-intrinsic functions, particularly aging, cancer, and pluripotency.
Published: 2023

2. High-repetition-rate ultrafast source emitting concomitantly in the 1.3 and 1.7 μm SWIR water-transparency bands for dual-color 3-photon microscopy

Author: Lamiae Abdeladim, Jean Livet, Karolis Jurkus, Marc Hanna, Frédéric Druon, Willy Supatto, Philippe Rigaud, Khmaies Guesmi, Pierre Mahou, Emmanuel Beaurepaire, Patrick Georges, Laboratoire Charles Fabry / Lasers, Laboratoire Charles Fabry (LCF), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS)-Institut d'Optique Graduate School (IOGS)-Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS)-Institut d'Optique Graduate School (IOGS), Laboratoire d'Optique et Biosciences (LOB), École polytechnique (X)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut de la Vision, Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Charles Fabry ( LCF ), Université Paris-Sud - Paris 11 ( UP11 ) -Institut d'Optique Graduate School ( IOGS ) -Centre National de la Recherche Scientifique ( CNRS ) -Université Paris-Sud - Paris 11 ( UP11 ) -Institut d'Optique Graduate School ( IOGS ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire d'Optique et Biosciences ( LOB ), École polytechnique ( X ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), and Université Paris-Sud - Paris 11 (UP11)-Institut d'Optique Graduate School (IOGS)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Sud - Paris 11 (UP11)-Institut d'Optique Graduate School (IOGS)-Centre National de la Recherche Scientifique (CNRS)
Subjects: [PHYS.PHYS.PHYS-OPTICS]Physics [physics]/Physics [physics]/Optics [physics.optics], Photon, Materials science, [ PHYS.PHYS.PHYS-OPTICS ] Physics [physics]/Physics [physics]/Optics [physics.optics], Repetition (rhetorical device), business.industry, 02 engineering and technology, 021001 nanoscience & nanotechnology, Laser, 01 natural sciences, law.invention, 010309 optics, law, 0103 physical sciences, Microscopy, Optoelectronics, 0210 nano-technology, Biological imaging, business, Dual color, Ultrashort pulse, Excitation
Abstract: International audience; We present a novel ultrafast laser design providing simultaneous excitation in the two water-transparency windows at 1.3 and 1.7 µm, and we demonstrate its potentiality for efficient 3-photon microscopy of nervous tissues.
Published: 2017

3. Multicolor two-photon imaging of endogenous fluorophores in living tissues by wavelength mixing

Author: Ana-Maria Pena, Guy Malkinson, Isabelle Lamarre, Sébastien Brizion, Xavier Solinas, Pierre Mahou, Lamiae Abdeladim, Willy Supatto, Renaud Legouis, Chiara Stringari, Jean-Baptiste Galey, Emmanuel Beaurepaire, Laboratoire d'Optique et Biosciences ( LOB ), École polytechnique ( X ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), L'Oréal Recherche, L'OREAL, Institut de Biologie Intégrative de la Cellule ( I2BC ), Université Paris-Sud - Paris 11 ( UP11 ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ), Roura, Denis, Laboratoire d'Optique et Biosciences (LOB), École polytechnique (X)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Intégrative de la Cellule (I2BC), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)
Subjects: [PHYS.PHYS.PHYS-OPTICS] Physics [physics]/Physics [physics]/Optics [physics.optics], 0301 basic medicine, Fluorescence-lifetime imaging microscopy, [SDV.IB.IMA]Life Sciences [q-bio]/Bioengineering/Imaging, Science, Biology, Nicotinamide adenine dinucleotide, 7. Clean energy, Article, Cofactor, Retinoids, 03 medical and health sciences, chemistry.chemical_compound, Two-photon excitation microscopy, Animals, Humans, Caenorhabditis elegans, [ SDV.IB.IMA ] Life Sciences [q-bio]/Bioengineering/Imaging, Skin, Flavin adenine dinucleotide, [PHYS.PHYS.PHYS-OPTICS]Physics [physics]/Physics [physics]/Optics [physics.optics], [ PHYS.PHYS.PHYS-OPTICS ] Physics [physics]/Physics [physics]/Optics [physics.optics], Multidisciplinary, Fibroblasts, Fluorescence, Electron transport chain, Microscopy, Fluorescence, Multiphoton, [SDV.IB.IMA] Life Sciences [q-bio]/Bioengineering/Imaging, 030104 developmental biology, chemistry, Biochemistry, Flavin-Adenine Dinucleotide, Biophysics, biology.protein, Medicine, NAD+ kinase, NADP
Abstract: International audience; Two-photon imaging of endogenous fluorescence can provide physiological and metabolic information from intact tissues. However, simultaneous imaging of multiple intrinsic fluorophores, such as nicotinamide adenine dinucleotide(phosphate) (NAD(P)H), flavin adenine dinucleotide (FAD) and retinoids in living systems is generally hampered by sequential multi-wavelength excitation resulting in motion artifacts. Here, we report on efficient and simultaneous multicolor two-photon excitation of endogenous fluorophores with absorption spectra spanning the 750–1040 nm range, using wavelength mixing. By using two synchronized pulse trains at 760 and 1041 nm, an additional equivalent two-photon excitation wavelength at 879 nm is generated, and achieves simultaneous excitation of blue, green and red intrinsic fluorophores. This method permits an efficient simultaneous imaging of the metabolic coenzymes NADH and FAD to be implemented with perfect image co-registration, overcoming the difficulties associated with differences in absorption spectra and disparity in concentration. We demonstrate ratiometric redox imaging free of motion artifacts and simultaneous two-photon fluorescence lifetime imaging (FLIM) of NADH and FAD in living tissues. The lifetime gradients of NADH and FAD associated with different cellular metabolic and differentiation states in reconstructed human skin and in the germline of live C. Elegans are thus simultaneously measured. Finally, we present multicolor imaging of endogenous fluorophores and second harmonic generation (SHG) signals during the early stages of Zebrafish embryo development, evidencing fluorescence spectral changes associated with development. Multiphoton microscopy is a powerful tool for label-free and non-invasive functional imaging in small organisms and tissues 1, 2. Pulsed near infrared excitation light allows in-depth imaging based on contrasts such as endog-enous fluorescence 2 , second harmonic generation (SHG) 3 and third harmonic generation (THG) 4. Endogenous fluorescence in living tissues arises from several intrinsic biomarkers that play important roles in physiological processes 2. The primary intracellular sources are NAD(P)H and FAD, the two major cofactors of redox reactions in the cell and central regulators of energy production and metabolism 5, 6. Their fluorescence reports on the metabolic activity of cells allowing tissue physiology and processes such as stem cell differentiation, cancer development and neurodegenerative diseases to being non-invasively monitored 7–12. The fluorescence lifetimes of NADH and FAD are different upon binding to the protein during the electron transport chain. FLIM provides sensitive measurements of the free and protein-bound NAD(P)H ratio and of the redox states (NADH/NAD +) of cells, and can be used to distinguish glycolytic and oxidative phosphorylation metabolic states 13–17. Monitoring lifetime of free and protein-bound FAD has also been exploited to quantify redox ratio FAD/FADH 2 , and used as a biomarker of precancerous epithelial cells 12. It is well established that retinoids play a crucial role in stem cell differentiation and embryo development 18, 19 and their concentration and gradients have been detected in vivo during zebrafish development 9, 20. Other intrinsic fluorophores such as porphyrin, collagen, elastin, keratin
Published: 2017

4. Conformational dynamics of G-quadruplex DNA probed by time-resolved circular dichroism

Author: Schmid, Marco, STAR, ABES, Laboratoire d'Optique et Biosciences ( LOB ), École polytechnique ( X ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Université Paris-Saclay, François Hache, Pascale Changenet-Barret, Laboratoire d'Optique et Biosciences (LOB), École polytechnique (X)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), and Université Paris Saclay (COmUE)
Subjects: G-Quadruplexes, [PHYS.PHYS.PHYS-OPTICS] Physics [physics]/Physics [physics]/Optics [physics.optics], [PHYS.PHYS.PHYS-OPTICS]Physics [physics]/Physics [physics]/Optics [physics.optics], Fs time resolution, Resolu en temps, [ PHYS.PHYS.PHYS-OPTICS ] Physics [physics]/Physics [physics]/Optics [physics.optics], Circular dichroism, Dichroisme circulaire
Abstract: Guanine-quadruplexes (G4) are non-canonical DNA structures that result from the hydrophobic stacking of guanine quartets stabilized by metal cations (typically Na+ and K+). There is now an increasing body of experimental evidence of their occurrence in important cell functions correlated to their folding/unfolding mechanisms. However, only few studies have addressed the dynamical aspect of their formation. In this context, we have undertaken the study of several intramolecular G4 with a novel extension of temperature-jump experiments capable to measure the thermal denaturation and the consecutive renaturation of DNA over a time window spanning a few ten milliseconds to seconds. Conformational changes have been monitored by time-resolved circular dichroism (CD), which is known to be sensitive to the chiral arrangement of guanines in the G4 scaffolds.Prior to time-resolved measurements, within the frame of a collaboration with DISCO/SOLEIL, we have performed static synchrotron radiation CD measurements on several short G4-forming sequences, such as human telomere, thrombin-binding aptamer and c-MYC promoter sequences, displaying distinct topologies. Denaturation and renaturation kinetics are found to exhibit biphasic decays with time constants of a few hundred milliseconds and a few seconds, respectively. Those kinetics depend strongly on the amplitude of the temperature jump and the concentration of cations. Taken together these observations suggest the existence of multiple folding pathways on extremely rugged landscapes., Les quadruplexes de guanines (G4) sont des structures d’ADN non-canoniques qui résultent de l’empilement hydrophobe de tétrades de guanines, stabilisé par des cations métalliques (tels que Na+ et K+). Il existe aujourd’hui un nombre croissant de preuves expérimentales qui attestent de l’implication des G4 dans d’importantes fonctions cellulaires corrélées à leur mécanisme de repliement/dépliement. Toutefois, très peu d’études ont abordé les aspects dynamiques de leur formation. Aussi, nous avons entrepris l’étude de plusieurs G4 mono-moléculaires à l’aide d’une nouvelle extension d’expériences de saut de température, capable de mesurer la dynamique de dénaturation thermique et de renaturation consécutive de l’ADN, sur une fenêtre temporelle allant de quelques millisecondes aux secondes. Les changements conformationnels ont été sondés par dichroïsme circulaire (CD) résolu en temps, connu pour être très sensible à l’arrangement des guanines dans les G4. Au préalable des études résolues en temps, en collaboration avec DISCO/SOLEIL, nous avons mesuré les spectres CD statiques de différentes séquences G4 présentant des topologies distinctes, comme celles des télomères humains, de l’aptamère de la thrombine ou des promoteurs de c-MYC. Nous avons observé des cinétiques de dénaturation et renaturation biphasiques avec des constantes de temps de quelques centaines de millisecondes et quelques secondes. Ces cinétiques dépendent fortement de l’amplitude du saut de température et de la concentration de cations métalliques. L’ensemble de ces observations suggère l’existence de plusieurs voies de repliement/dépliement des G4 sur des surfaces de potentiel très rugueuses.
Published: 2017

5. Regulation of the ROS Response Dynamics and Organization to PDGF Motile Stimuli Revealed by Single Nanoparticle Imaging

Author: Antigoni Alexandrou, Rivo Ramodiharilafy, Cedric Bouzigues, Pierre-Louis Tharaux, Thanh-Liem Nguyen, Amy A. Claeson, Laboratoire d'optique et biosciences (LOB), École polytechnique (X)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Paris-Centre de Recherche Cardiovasculaire (PARCC - UMR-S U970), Université Paris Descartes - Paris 5 (UPD5)-Hôpital Européen Georges Pompidou [APHP] (HEGP), Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratoire d'optique et biosciences ( LOB ), École polytechnique ( X ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Paris-Centre de Recherche Cardiovasculaire ( PARCC - U970 ), Hôpital Européen Georges Pompidou [APHP] ( HEGP ) -Université Paris Descartes - Paris 5 ( UPD5 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ), Hôpital Européen Georges Pompidou [APHP] (HEGP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Hôpital Européen Georges Pompidou [APHP] (HEGP), and Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)
Subjects: Male, [PHYS.PHYS.PHYS-BIO-PH]Physics [physics]/Physics [physics]/Biological Physics [physics.bio-ph], medicine.medical_treatment, Clinical Biochemistry, Biochemistry, [ SDV.BC.IC ] Life Sciences [q-bio]/Cellular Biology/Cell Behavior [q-bio.CB], Mice, [ PHYS.PHYS.PHYS-BIO-PH ] Physics [physics]/Physics [physics]/Biological Physics [physics.bio-ph], Cell surface receptor, [SDV.BC.IC]Life Sciences [q-bio]/Cellular Biology/Cell Behavior [q-bio.CB], Drug Discovery, medicine, Animals, Humans, Kinase activity, Molecular Biology, Cells, Cultured, Platelet-Derived Growth Factor, Pharmacology, chemistry.chemical_classification, Reactive oxygen species, biology, Growth factor, Hydrogen Peroxide, General Medicine, Cell biology, Mice, Inbred C57BL, chemistry, Cancer cell, Second messenger system, biology.protein, Nanoparticles, Molecular Medicine, Signal transduction, Reactive Oxygen Species, Platelet-derived growth factor receptor, HeLa Cells, Signal Transduction
Abstract: International audience; Although reactive oxygen species (ROS) are better known for their harmful effects, more recently, H2O2, one of the ROS, was also found to act as a secondary messenger. However, details of spatiotemporal organization of specific signaling pathways that H2O2 is involved in are currently missing. Here, we use single nanoparticle imaging to measure the local H2O2 concentration and reveal regulation of the ROS response dynamics and organization to platelet-derived growth factor (PDGF) signaling. We demonstrate that H2O2 production is controlled by PDGFR kinase activity and EGFR transactivation, requires a persistent stimulation, and is regulated by membrane receptor diffusion. This temporal filtering is impaired in cancer cells, which may determine their pathological migration. H2O2 subcellular mapping reveals that an external PDGF gradient induces an amplification-free asymmetric H2O2 concentration profile. These results support a general model for the control of signal transduction based only on membrane receptor diffusion and second messenger degradation.
Published: 2014

6. Exploring Sequence Space to Design Controllable G-Quadruplex Topology Switches

Author: Jean-Louis Mergny, Petr Stadlbauer, Jielin Chen, Jiří Šponer, Jun Zhou, Mingpan Cheng, Huangxian Ju, Nanjing University (NJU), Institute of Biophysics of the Czech Academy of Sciences (IBP / CAS), Czech Academy of Sciences [Prague] (CAS), Laboratoire d'Optique et Biosciences (LOB), École polytechnique (X)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Mergny, Jean-Louis, and Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École polytechnique (X)
Subjects: Regulation of gene expression, Physics, [CHIM.ANAL] Chemical Sciences/Analytical chemistry, G-quadruplex, 010405 organic chemistry, [SDV.BBM.BP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, General Chemistry, 010402 general chemistry, Topology, 01 natural sciences, Sequence space, 0104 chemical sciences, [SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, G-quadruplex topology, structural versatility, [CHIM.ANAL]Chemical Sciences/Analytical chemistry, Nucleic acid, sequence composition, heterocyclic compounds, Gswitch, human activities, Topology (chemistry)
Abstract: International audience; As nonclassical nucleic acid structures, G-quadruplexes (G4s) not only play important roles in gene regulation and stability maintenance, but are also widely used in nanotechnology. Structural diversity is one of the main factors explaining the popularity of G4s, but a comprehensive and integrated study of different factors determining G4 structural versatility is currently lacking. Herein, starting from a common G4 sequence, (G 3 T) 3 G 3 , as the parent chain, and then taking advantage of G4 versatility, we present a variety of strategies to control G4 structure, based on the regulation of loop length and flanking sequences, cation (type and concentration), and molecular crowding. These strategies allow us to convert the G4 topology from parallel to hybrid, to antiparallel, and then back to parallel. Such structural diversity reveals the coding regulation ability of G4 structures, with potential applications in nanotechnology.
Published: 2022

7. G4access identifies G-quadruplexes and their associations with open chromatin and imprinting control regions

Author: Esnault, Cyril, Magat, Talha, Zine El Aabidine, Amal, Garcia-Oliver, Encar, Cucchiarini, Anne, Bouchouika, Soumya, Lleres, David, Goerke, Lutz, Luo, Yu, Verga, Daniela, Lacroix, Laurent, Feil, Robert, Spicuglia, Salvatore, Mergny, Jean‐louis, Andrau, Jean-Christophe, Institut de Génétique Moléculaire de Montpellier (IGMM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Laboratoire d'Optique et Biosciences (LOB), École polytechnique (X)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Chimie et modélisation pour la biologie du cancer (CMBC), Institut Curie [Paris]-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), Institut de biologie de l'Ecole Normale Supérieure (IBENS), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Aix-Marseille Université - Faculté des Sciences (AMU SCI), Aix Marseille Université (AMU), and ANR-20-CE12-0023,G4Access,Role des G-quadruplexes dans la régulation transcriptionnelle(2020)
Subjects: [SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, G-quadruplex, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], transcription
Abstract: International audience; Metazoan promoters are enriched in secondary DNA structure-forming motifs, such as G-quadruplexes (G4s). Here we describe ‘G4access’, an approach to isolate and sequence G4s associated with open chromatin via nuclease digestion. G4access is antibody- and crosslinking-independent and enriches for computationally predicted G4s (pG4s), most of which are confirmed in vitro. Using G4access in human and mouse cells, we identify cell-type-specific G4 enrichment correlated with nucleosome exclusion and promoter transcription. G4access allows measurement of variations in G4 repertoire usage following G4 ligand treatment, HDAC and G4 helicases inhibitors. Applying G4access to cells from reciprocal hybrid mouse crosses suggests a role for G4s in the control of active imprinting regions. Consistently, we also observed that G4access peaks are unmethylated, while methylation at pG4s correlates with nucleosome repositioning on DNA. Overall, our study provides a new tool for studying G4s in cellular dynamics and highlights their association with open chromatin, transcription and their antagonism to DNA methylation.
Published: 2023

8. DNA topoisomerase 1 represses HIV-1 promoter activity through its interaction with a guanine quadruplex present in the LTR sequence

Author: Lista, María José, Jousset, Anne-Caroline, Cheng, Mingpan, Saint-André, Violaine, Perrot, Elouan, Rodrigues, Melissa, Di Primo, Carmelo, Gadelle, Danielle, Toccafondi, Elenia, Segeral, Emmanuel, Berlioz-Torrent, Clarisse, Emiliani, Stéphane, Mergny, Jean-Louis, Lavigne, Marc, Institut Cochin (IC UM3 (UMR 8104 / U1016)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Acides Nucléiques : Régulations Naturelle et Artificielle (ARNA), Université de Bordeaux (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité), Département de Virologie - Department of Virology, 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), Laboratoire d'Optique et Biosciences (LOB), École polytechnique (X)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), and This work was supported by Sidaction [AO 2017-2 and AO 2020-1 to ML], the ANRS [AO 2014-2 CSS2 and AO 2019-1 CSS11 to ML]. MJL is a recipient of an ANRS postdoctoral fellowship. ACJ, EP and MR are recipients of Research Engineer or Technician contracts from Sidaction.
Subjects: Transcriptional regulation, HIV-1 LTR promoter, DNA topoisomerases, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, HIV-1 transcription, HIV-1 latency, Guanine quadruplex, Host-virus interaction
Abstract: Background: Once integrated in the genome of infected cells, HIV-1 provirus is transcribed by the cellular transcription machinery. This process is regulated by both viral and cellular factors, which are necessary for an efficient viral replication as well as for the setting up of viral latency, leading to a repressed transcription of the integrated provirus.Results: In this study, we examined the role of two parameters in HIV-1 LTR promoter activity. We identified DNA topoisomerase1 (TOP1) to be a potent repressor of this promoter and linked this repression to its catalytic domain. Additionally, we confirmed the folding of a Guanine quadruplex (G4) structure in the HIV-1 promoter and its repressive effect. We demonstrated a direct interaction between TOP1 and this G4 structure, providing evidence of a functional relationship between the two repressive elements. Mutations abolishing G4 folding affected TOP1/G4 interaction and hindered G4-dependent inhibition of TOP1 catalytic activity in vitro. As a result, HIV-1 promoter activity was reactivated in a native chromatin environment. Lastly, we noticed an enrichment of predicted G4 sequences in the promoter of TOP1-repressed cellular genes.Conclusions: Our results demonstrate the formation of a TOP1/G4 complex on the HIV-1 LTR promoter and its repressive effect on the promoter activity. They reveal the existence of a new mechanism of TOP1/G4-dependent transcriptional repression conserved between viral and human genes. This mechanism contrasts with the known property of TOP1 as global transcriptional activator and offers new perspectives for anti-cancer and anti-viral strategies.
Published: 2023

9. Autocatalytic effect boosts the production of medium-chain hydrocarbons by fatty acid photodecarboxylase

Author: Poutoum P. Samire, Bo Zhuang, Bertrand Légeret, Ángel Baca-Porcel, Gilles Peltier, Damien Sorigué, Alexey Aleksandrov, Frédéric Beisson, Pavel Müller, Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB) (BIAM), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-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 d'Optique et Biosciences (LOB), École polytechnique (X)-Institut National de la Santé et de la Recherche Médicale (INSERM)-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), Département Biochimie, Biophysique et Biologie Structurale (B3S), 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), China Scholarship Council, ANR-18-CE11-0021,SNAPsHOTs,Dynamique structurale de l'acide gras photodécarboxylase(2018), ANR-18-CE43-0008,PHOTOALKANE,Production biosourcée d'hydrocarbures basée sur une nouvelle photoenzyme(2018), and ANR-18-CE44-0002,ATMCADD,Modèles atomiques précis pour la conception de médicaments assistée par ordinateur(2018)
Subjects: Multidisciplinary, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, [CHIM.CATA]Chemical Sciences/Catalysis
Abstract: Ongoing climate change is driving the search for renewable and carbon-neutral alternatives to fossil fuels. Photocatalytic conversion of fatty acids to hydrocarbons by fatty acid photodecarboxylase (FAP) represents a promising route to green fuels. However, the alleged low activity of FAP on C2 to C12 fatty acids seemed to preclude the use for synthesis of gasoline-range hydrocarbons. Here, we reveal that Chlorella variabilis FAP ( Cv FAP) can convert n -octanoic acid in vitro four times faster than n -hexadecanoic acid, its best substrate reported to date. In vivo, this translates into a Cv FAP-based production rate over 10-fold higher for n -heptane than for n -pentadecane. Time-resolved spectroscopy and molecular modeling demonstrate that Cv FAP’s high catalytic activity on n -octanoic acid is, in part, due to an autocatalytic effect of its n -heptane product, which fills the rest of the binding pocket. These results represent an important step toward a bio-based and light-driven production of gasoline-like hydrocarbons.
Published: 2023

10. Origines bactériennes du métabolisme du thymidylate chez les archées Asgard et Eukarya: Évolution de l'ADN

Author: Jonathan Filée, Hubert F. Becker, Lucille Mellottee, Rima Zein Eddine, Zhihui Li, Wenlu Yin, Jean-Christophe Lambry, Ursula Liebl, Hannu Myllykallio, Evolution, génomes, comportement et écologie (EGCE), Institut de Recherche pour le Développement (IRD)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Optique et Biosciences (LOB), École polytechnique (X)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), and W.Y. is a recipient of a doctoral grant from China ScholarshipCouncil (CSC).
Subjects: Asgard, Multidisciplinary, [SDV]Life Sciences [q-bio], General Physics and Astronomy, evololution, General Chemistry, Archaea, thymidylate and folate metabolism, General Biochemistry, Genetics and Molecular Biology
Abstract: International audience; Asgard archaea include the closest known archaeal relatives of eukaryotes. Here, we investigate the evolution and function of Asgard thymidylate synthases and other folate-dependent enzymes required for the biosynthesis of DNA, RNA, amino acids and vitamins, as well as syntrophic amino acid utilization. Phylogenies of Asgard folate-dependent enzymes are consistent with their horizontal transmission from various bacterial groups. We experimentally validate the functionality of thymidylate synthase ThyX of the cultured 'Candidatus Prometheoarchaeum syntrophicum'. The enzyme efficiently uses bacterial-like folates and is inhibited by mycobacterial ThyX inhibitors, even though the majority of experimentally tested archaea are known to use carbon carriers distinct from bacterial folates. Our phylogenetic analyses suggest that the eukaryotic thymidylate synthase, required for de novo DNA synthesis, is not closely related to archaeal enzymes and might have been transferred from bacteria to protoeukaryotes during eukaryogenesis. Altogether, our study suggests that the capacity of eukaryotic cells to duplicate their genetic material is a sum of archaeal (replisome) and bacterial (thymidylate synthase) characteristics. We also propose that recent prevalent lateral gene transfer from bacteria has markedly shaped the metabolism of Asgard archaea.; Les archées Asgard sont les plus proches parents connus des eucaryotes. Nous étudions ici l'évolution et la fonction des thymidylate synthases d'Asgard et d'autres enzymes folate-dépendantes nécessaires à la biosynthèse de l'ADN, de l'ARN, des acides aminés et des vitamines, ainsi que l'utilisation syntrophique des acides aminés. Les phylogénies des enzymes folate-dépendantes d'Asgard sont cohérentes avec leur transmission horizontale à partir de divers groupes bactériens. Nous validons expérimentalement la fonctionnalité de la thymidylate synthase ThyX de la culture 'Candidatus Prometheoarchaeum syntrophicum'. L'enzyme utilise efficacement des folates de type bactérien et est inhibée par les inhibiteurs ThyX mycobactériens, même si la majorité des archées testées expérimentalement sont connues pour utiliser des transporteurs de carbone distincts des folates bactériens. Nos analyses phylogénétiques suggèrent que la thymidylate synthase eucaryote, nécessaire à la synthèse de novo de l'ADN, n'est pas étroitement liée aux enzymes archéales et pourrait avoir été transférée des bactéries aux protoeucaryotes pendant l'eucaryogenèse. Dans l'ensemble, notre étude suggère que la capacité des cellules eucaryotes à dupliquer leur matériel génétique est une somme de caractéristiques archéennes (replisome) et bactériennes (thymidylate synthase). Nous proposons également que le transfert latéral de gènes prévalant récemment à partir de bactéries a façonné de façon marquée le métabolisme des archées asgardes.
Published: 2023

11. In situ determination of collagen fibrils size via absolute measurements of second harmonic generation signals

Author: Stéphane Bancelin, Carole Aimé, Ivan Gusachenko, Laura Kowalczuk, Gael Latour, Thibaud Coradin, Marie-Claire Schanne-Klein, Laboratoire d'Optique et Biosciences (LOB), École polytechnique (X)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Matériaux et Biologie (MATBIO), Laboratoire de Chimie de la Matière Condensée de Paris (LCMCP), Université Pierre et Marie Curie - Paris 6 (UPMC)-Collège de France (CdF (institution))-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Collège de France (CdF (institution))-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Centre de Recherche des Cordeliers (CRC (UMR_S 872)), Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Collège de France (CdF (institution))-Institut de Chimie du CNRS (INC)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Collège de France (CdF (institution))-Institut de Chimie du CNRS (INC), Université Paris Descartes - Paris 5 (UPD5)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Optique et Biosciences ( LOB ), École polytechnique ( X ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Matériaux et Biologie ( MATBIO ), Laboratoire de Chimie de la Matière Condensée de Paris ( LCMCP ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Collège de France ( CdF ) -Centre National de la Recherche Scientifique ( CNRS ) -Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Collège de France ( CdF ) -Centre National de la Recherche Scientifique ( CNRS ), Centre de Recherche des Cordeliers ( CRC (UMR_S 872) ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Université Paris Descartes - Paris 5 ( UPD5 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École polytechnique (X), and Université Pierre et Marie Curie - Paris 6 (UPMC)-Collège de France (CdF)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Collège de France (CdF)-Centre National de la Recherche Scientifique (CNRS)
Subjects: [SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, [ SDV.BBM.BP ] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, [PHYS.PHYS.PHYS-OPTICS]Physics [physics]/Physics [physics]/Optics [physics.optics], [ PHYS.PHYS.PHYS-OPTICS ] Physics [physics]/Physics [physics]/Optics [physics.optics], animal structures, [SDV.IB.IMA]Life Sciences [q-bio]/Bioengineering/Imaging, sense organs, [ SDV.IB.IMA ] Life Sciences [q-bio]/Bioengineering/Imaging
Abstract: International audience; We correlated SHG and Electron Microscopies to calibrate SHG signals as a function of collagen fibril diameter, down to 30 nm. We observed a fourth power dependence, in agreement with analytical and numerical calculations. We applied this calibration to abnormal fibrils in the Descemet’s membrane of intact unfixed rat corneas.
Published: 2015

12. Circulating cell membrane microparticles transfer heme to endothelial cells and trigger vasoocclusions in sickle cell disease

Author: Alain Tedgui, Philippe Bonnin, Sylvain Le Jeune, João Alfredo Moraes, Laurent Kiger, Hervé Le Clésiau, Olivier Blanc-Brude, Laurent Loufrani, Claire Larroque, Antigoni Alexandrou, Christina Barja-Fidalgo, Paul Abbyad, Pierre-Louis Tharaux, Chantal M. Boulanger, Stéphane M. Camus, Patrick Bruneval, Jean-Marie Renard, Jean-Christophe Lambry, Dominique Charue, François Lionnet, Linda Grimaud, Architecture, Urbanisme, Sociétés (AUS), Université Paris 8 Vincennes-Saint-Denis (UP8)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Ecole d'architecture Paris-Malaquais-Ecole d'architecture Paris-Belleville-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Laboratoire d'optique et biosciences (LOB), École polytechnique (X)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), CHU Tenon [APHP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université, Biologie Neurovasculaire Intégrée (BNVI), Université d'Angers (UA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche en Génie Civil et Mécanique (GeM), Université de Nantes - Faculté des Sciences et des Techniques, Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS), Paris-Centre de Recherche Cardiovasculaire (PARCC - UMR-S U970), Hôpital Européen Georges Pompidou [APHP] (HEGP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Substitut du sang et pathologie moléculaire du globule rouge, Institut National de la Santé et de la Recherche Médicale (INSERM), Evaluation des technologies de santé et des pratiques médicales - ULR 2694 (METRICS), Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), Laboratoire de Recherche en Imagerie : Méthodes d'imagerie des Échanges transcapillaires (LRI - EA4062), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratorio de Farmacologia Celular e Molecular [Rio de Janeiro, Brazil], Universidade do Estado do Rio de Janeiro [Rio de Janeiro] (UERJ), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Hôpital Européen Georges Pompidou [APHP] (HEGP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO), Carcinose Angiogenèse et Recherche Translationnelle, Angiogenese et recherche translationnelle (CART U965), Université Paris Diderot - Paris 7 (UPD7)-Institut National de la Santé et de la Recherche Médicale (INSERM), Hôpital Avicenne [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), CHU Tenon [AP-HP], Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Biologie Neurovasculaire et Mitochondriale Intégrée (BNMI), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université d'Angers (UA), Centre Hospitalier Universitaire d'Angers (CHU Angers), PRES Université Nantes Angers Le Mans (UNAM), Laboratoire d'Optique et Biosciences (LOB), Hôpital Henri Mondor, Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Henri Mondor-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Caisse Primaire Assurance Maladie, Hlth Appraisal Ctr, Université Paris Nanterre (UPN)-Ecole d'architecture Paris-Malaquais-Université Paris 8 Vincennes-Saint-Denis (UP8)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Ecole d'architecture Paris-Belleville-Ministère de la Culture et de la Communication (MCC), Université Paris Descartes - Paris 5 (UPD5)-Hôpital Européen Georges Pompidou [APHP] (HEGP), Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Institut National de la Santé et de la Recherche Médicale (INSERM), Santé publique : épidémiologie et qualité des soins-EA 2694 (CERIM), Paris-Centre de Recherche Cardiovasculaire ( PARCC - U970 ), Université Paris Descartes - Paris 5 ( UPD5 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Hôpital Européen Georges Pompidou [APHP] ( HEGP ), Angiogenese et recherche translationnelle ( CART U965 ), Université Paris Diderot - Paris 7 ( UPD7 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ), Laboratoire d'optique et biosciences ( LOB ), École polytechnique ( X ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Hôpital avicenne, Université Paris 13 ( UP13 ) -Assistance publique - Hôpitaux de Paris (AP-HP)-Hôpital Avicenne, Biologie Neurovasculaire et Mitochondriale Intégrée, Université d'Angers ( UA ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Centre Hospitalier Universitaire d'Angers ( CHU Angers ), PRES Université Nantes Angers Le Mans ( UNAM ), Laboratoire d'Optique et Biosciences ( LOB ), Assistance publique - Hôpitaux de Paris (AP-HP)-Hôpital Henri Mondor-Université Paris-Est Créteil Val-de-Marne - Paris 12 ( UPEC UP12 ), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Paris 13 (UP13)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Avicenne [AP-HP], Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École polytechnique (X), Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Institut National de la Santé et de la Recherche Médicale (INSERM), Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Université Paris 13 (UP13)-Hôpital Avicenne, Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Hôpital Henri Mondor-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), and Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)
Subjects: Male, Erythrocytes, Cell, 030204 cardiovascular system & hematology, Biochemistry, Cohort Studies, Cell membrane, Mice, chemistry.chemical_compound, 0302 clinical medicine, Cell-Derived Microparticles, Medicine, [ SDV.MHEP.HEM ] Life Sciences [q-bio]/Human health and pathology/Hematology, skin and connective tissue diseases, Heme, ComputingMilieux_MISCELLANEOUS, 0303 health sciences, Hemopexin, [SDV.MHEP.HEM]Life Sciences [q-bio]/Human health and pathology/Hematology, Hematology, Phosphatidylserine, Hemolysis, 3. Good health, Cell biology, medicine.anatomical_structure, congenital, hereditary, and neonatal diseases and abnormalities, Endothelium, Immunology, Anemia, Sickle Cell, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, 03 medical and health sciences, Vascular Biology, [SDV.MHEP.PHY]Life Sciences [q-bio]/Human health and pathology/Tissues and Organs [q-bio.TO], Animals, Humans, Vascular Diseases, 030304 developmental biology, business.industry, [ SDV.BC ] Life Sciences [q-bio]/Cellular Biology, Endothelial Cells, nutritional and metabolic diseases, Cell Biology, medicine.disease, Mice, Inbred C57BL, Oxidative Stress, chemistry, business, Ex vivo
Abstract: International audience; Intravascular hemolysis describes the relocalization of heme and hemoglobin (Hb) from erythrocytes to plasma. We investigated the concept that erythrocyte membrane microparticles (MPs) concentrate cell-free heme in human hemolytic diseases, and that hemeladen MPs have a physiopathological impact. Up to one-third of cell-free heme in plasma from 47 patients with sickle cell disease (SCD) was sequestered in circulating MPs. Erythrocyte vesiculation in vitro produced MPs loaded with heme. In silico analysis predicted that externalized phosphatidylserine (PS) in MPs may associate with and help retain heme at the cell surface. Immunohistology identified Hb-laden MPs adherent to capillary endothelium in kidney biopsies from hyperalbuminuric SCD patients. In addition, heme-laden erythrocyte MPs adhered and transferred heme to cultured endothelial cells, inducing oxidative stress and apoptosis. In transgenic SAD mice, infusion of hemeladen MPs triggered rapid vasoocclusions in kidneys and compromised microvascular dilation ex vivo. These vascular effects were largely blocked by heme-scavenging hemopexin and by the PS antagonist annexin-a5, in vitro and in vivo. Adversely remodeled MPs carrying heme may thus be a source of oxidant stress for the endothelium, linking hemolysis to vascular injury. This pathway might provide new targets for the therapeutic preservation of vascular function in SCD.
Published: 2015

13. ROS Detection and Quantification with Lanthanide-Based Nanosensors

Author: Pierre-Louis Tharaux, Antigoni Alexandrou, Jean-Pierre Boilot, Mouna Abdesselem, Thierry Gacoin, Cedric Bouzigues, Laboratoire d'optique et biosciences (LOB), École polytechnique (X)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de physique de la matière condensée (LPMC), École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS), Paris-Centre de Recherche Cardiovasculaire (PARCC - UMR-S U970), Hôpital Européen Georges Pompidou [APHP] (HEGP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Biophysical society, Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Hôpital Européen Georges Pompidou [APHP] (HEGP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO), Université Paris Descartes - Paris 5 (UPD5)-Hôpital Européen Georges Pompidou [APHP] (HEGP), Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratoire d'optique et biosciences ( LOB ), École polytechnique ( X ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de physique de la matière condensée ( LPMC ), École polytechnique ( X ) -Centre National de la Recherche Scientifique ( CNRS ), Paris-Centre de Recherche Cardiovasculaire ( PARCC - U970 ), and Hôpital Européen Georges Pompidou [APHP] ( HEGP ) -Université Paris Descartes - Paris 5 ( UPD5 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM )
Subjects: chemistry.chemical_classification, Reactive oxygen species, [PHYS.PHYS.PHYS-OPTICS]Physics [physics]/Physics [physics]/Optics [physics.optics], [ PHYS.PHYS.PHYS-OPTICS ] Physics [physics]/Physics [physics]/Optics [physics.optics], Biophysics, Nanotechnology, 04 agricultural and veterinary sciences, Biology, medicine.disease_cause, 040401 food science, 01 natural sciences, 0104 chemical sciences, Cell biology, Multiple pathologies, 010404 medicinal & biomolecular chemistry, chemistry.chemical_compound, 0404 agricultural biotechnology, chemistry, Nanosensor, medicine, Signal transduction, Hydrogen peroxide, Oxidative stress
Abstract: International audience; Reactive oxygen species (ROS), in particular hydrogen peroxide (H2O2), are produced as secondary cellular messengers involved in a variety of signaling pathways. Detecting ROS concentration in cells and in living organisms is particularly important because ROS oxidative stress plays a complex role in multiple pathologies: inflammatory processes, neurodegenerative diseases, and cancer. We first report on an europium-based H2O2 sensor (Y0.6Eu0.4VO4) that shows red, oxidant-dependant, reversible luminescence modulation used in cells in culture.
Published: 2015

14. Multifunctional rare-Earth vanadate nanoparticles: luminescent labels, oxidant sensors, and MRI contrast agents

Author: Rivo Ramodiharilafy, Gwennhael Autret, Olivier Clément, Pierre-Louis Tharaux, Mouna Abdesselem, Isabelle Maurin, Markus Schoeffel, Cedric Bouzigues, Thierry Gacoin, Jean-Pierre Boilot, Antigoni Alexandrou, Laboratoire d'optique et biosciences ( LOB ), École polytechnique ( X ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de physique de la matière condensée ( LPMC ), École polytechnique ( X ) -Centre National de la Recherche Scientifique ( CNRS ), Paris-Centre de Recherche Cardiovasculaire ( PARCC - U970 ), Hôpital Européen Georges Pompidou [APHP] ( HEGP ) -Université Paris Descartes - Paris 5 ( UPD5 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ), Laboratoire d'optique et biosciences (LOB), École polytechnique (X)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de physique de la matière condensée (LPMC), École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS), Paris-Centre de Recherche Cardiovasculaire (PARCC - UMR-S U970), Hôpital Européen Georges Pompidou [APHP] (HEGP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Paris Descartes - Paris 5 (UPD5)-Hôpital Européen Georges Pompidou [APHP] (HEGP), Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Hôpital Européen Georges Pompidou [APHP] (HEGP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO), and Roura, Denis
Subjects: [PHYS.PHYS.PHYS-OPTICS] Physics [physics]/Physics [physics]/Optics [physics.optics], Luminescence, Materials science, [PHYS.PHYS.PHYS-BIO-PH]Physics [physics]/Physics [physics]/Biological Physics [physics.bio-ph], Inorganic chemistry, Contrast Media, General Physics and Astronomy, chemistry.chemical_element, Vanadium, Nanoparticle, 02 engineering and technology, 010402 general chemistry, 01 natural sciences, Ion, Mice, Paramagnetism, Microscopy, Electron, Transmission, [ PHYS.PHYS.PHYS-BIO-PH ] Physics [physics]/Physics [physics]/Biological Physics [physics.bio-ph], Spectroscopy, Fourier Transform Infrared, Animals, General Materials Science, Vanadate, [PHYS.PHYS.PHYS-OPTICS]Physics [physics]/Physics [physics]/Optics [physics.optics], [ PHYS.PHYS.PHYS-OPTICS ] Physics [physics]/Physics [physics]/Optics [physics.optics], [PHYS.PHYS.PHYS-BIO-PH] Physics [physics]/Physics [physics]/Biological Physics [physics.bio-ph], Relaxation (NMR), General Engineering, Yttrium, Oxidants, 021001 nanoscience & nanotechnology, Magnetic Resonance Imaging, 0104 chemical sciences, chemistry, Nanoparticles, Metals, Rare Earth, 0210 nano-technology
Abstract: International audience; Collecting information on multiple pathophysiological parameters is essential for understanding complex pathologies, especially given the large interindividual variability. We report here multifunctional nanoparticles which are luminescent probes, oxidant sensors, and contrast agents in magnetic resonance imaging (MRI). Eu(3+) ions in an yttrium vanadate matrix have been demonstrated to emit strong, nonblinking, and stable luminescence. Time- and space-resolved optical oxidant detection is feasible after reversible photoreduction of Eu(3+) to Eu(2+) and reoxidation by oxidants, such as H2O2, leading to a modulation of the luminescence emission. The incorporation of paramagnetic Gd(3+) confers in addition proton relaxation enhancing properties to the system. We synthesized and characterized nanoparticles of either 5 or 30 nm diameter with compositions of GdVO4 and Gd0.6Eu0.4VO4. These particles retain the luminescence and oxidant detection properties of YVO4:Eu. Moreover, the proton relaxivity of GdVO4 and Gd0.6Eu0.4VO4 nanoparticles of 5 nm diameter is higher than that of the commercial Gd(3+) chelate compound Dotarem at 20 MHz. Nuclear magnetic resonance dispersion spectroscopy showed a relaxivity increase above 10 MHz. Complexometric titration indicated that rare-earth leaching is negligible. The 5 nm nanoparticles injected in mice were observed with MRI to concentrate in the liver and the bladder after 30 min. Thus, these multifunctional rare-earth vanadate nanoparticles pave the way for simultaneous optical and magnetic resonance detection, in particular, for in vivo localization evolution and reactive oxygen species detection in a broad range of physiological and pathophysiological conditions.
Published: 2014

15. Label-free imaging of red blood cells and oxygenation with color third-order sum-frequency generation microscopy

Author: Júlia Ferrer Ortas, Pierre Mahou, Sophie Escot, Chiara Stringari, Nicolas B. David, Laure Bally-Cuif, Nicolas Dray, Michel Négrerie, Willy Supatto, Emmanuel Beaurepaire, Laboratoire d'Optique et Biosciences (LOB), École polytechnique (X)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Neurogénétique du Poisson zébré / Zebrafish Neurogenetics, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), European Research Council (Horizon 2020 programme, grant No 951330 HOPE). Agence Nationale de la Recherche (ANR) (ANR-EQPX-0029, ANR-10-INBS-04, ANR-10-LABX-0073). Fondation pour la Recherche Médicale (FRM) (DEI201512440). Ligue Nationale contre le Cancer., ANR-10-INBS-0004,France-BioImaging,Développment d'une infrastructure française distribuée coordonnée(2010), ANR-10-LABX-0073,REVIVE,Stem Cells in Regenerative Biology and Medicine(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), and European Project: 951330,NHMRC::NHMRC Project Grants(1995)
Subjects: [PHYS.PHYS.PHYS-OPTICS]Physics [physics]/Physics [physics]/Optics [physics.optics], Third harmonic generation, in vivo microscopy, Biological imaging, [SDV.IB.IMA]Life Sciences [q-bio]/Bioengineering/Imaging, [SDV]Life Sciences [q-bio], Third-order sum-frequency generation, Red blood cells, Tissue imaging, Atomic and Molecular Physics, and Optics, Multiphoton microscopy, Electronic, Optical and Magnetic Materials
Abstract: Mapping red blood cells (RBCs) flow and oxygenation is of key importance for analyzing brain and tissue physiology. Current microscopy methods are limited either in sensitivity or in spatio-temporal resolution. In this work, we introduce a novel approach based on label-free third-order sum-frequency generation (TSFG) and third-harmonic generation (THG) contrasts. First, we propose a novel experimental scheme for color TSFG microscopy, which provides simultaneous measurements at several wavelengths encompassing the Soret absorption band of hemoglobin. We show that there is a strong three-photon (3P) resonance related to the Soret band of hemoglobin in THG and TSFG signals from zebrafish and human RBCs, and that this resonance is sensitive to RBC oxygenation state. We demonstrate that our color TSFG implementation enables specific detection of flowing RBCs in zebrafish embryos and is sensitive to RBC oxygenation dynamics with single-cell resolution and microsecond pixel times. Moreover, it can be implemented on a 3P microscope and provides label-free RBC-specific contrast at depths exceeding 600 µm in live adult zebrafish brain. Our results establish a new multiphoton contrast extending the palette of deep-tissue microscopy.
Published: 2023

16. Evaluation of Slowfade Diamond as a buffer for STORM microscopy

Author: Hadjer Boukhatem, Beatrice Durel, Manon Raimbault, Audrey Laurent, Nicolas Olivier, Laboratoire d'Optique et Biosciences (LOB), École polytechnique (X)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut Polytechnique de Paris (IP Paris), Structure Fédérative de Recherche Necker (SFR Necker - UMS 3633 / US24), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Institut Necker Enfants-Malades (INEM - UM 111 (UMR 8253 / U1151)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), École Doctorale Bio Sorbonne Paris Cité [Paris] (ED562 - BioSPC), Université Sorbonne Paris Cité (USPC)-Université Paris Cité (UPCité), and Olivier, Nicolas
Subjects: [PHYS.PHYS.PHYS-OPTICS] Physics [physics]/Physics [physics]/Optics [physics.optics], [PHYS.PHYS.PHYS-OPTICS]Physics [physics]/Physics [physics]/Optics [physics.optics], [PHYS.PHYS.PHYS-INS-DET] Physics [physics]/Physics [physics]/Instrumentation and Detectors [physics.ins-det], [PHYS.PHYS.PHYS-INS-DET]Physics [physics]/Physics [physics]/Instrumentation and Detectors [physics.ins-det], Atomic and Molecular Physics, and Optics, Article, Biotechnology
Abstract: International audience; We study the potential of the commercial mounting medium Slowfade diamond as a buffer for STORM microscopy. We show that although it does not work with the popular far-red dyes typically used for STORM imaging, such as Alexa Fluor 647, it performs really well with a wide variety of green-excited dyes such as Alexa Fluor 532, Alexa Fluor 555 or CF 568. Moreover, imaging can be performed several months after the samples are mounted in this environment and kept in the fridge, providing a convenient way to preserve samples for STORM imaging, as well as to keep calibration samples, for example for metrology or teaching in particular in imaging facilities.
Published: 2023

17. Terahertz Spectroscopy Sheds Light on Real‐Time Exchange Kinetics Occurring through Plasma Membrane during Photodynamic Therapy Treatment

Author: Xiujun Zheng, Blandine Lordon, Anne‐Françoise Mingotaud, Patricia Vicendo, Rachel Brival, Isabelle Fourquaux, Laure Gibot, Guilhem Gallot, Laboratoire d'Optique et Biosciences (LOB), École polytechnique (X)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Interactions moléculaires et réactivité chimique et photochimique (IMRCP), Institut de Chimie de Toulouse (ICT), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Fédération de Recherche Fluides, Energie, Réacteurs, Matériaux et Transferts (FERMAT), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Centre de Microscopie Électronique Appliquée à la Biologie (CMEAB), Toulouse Réseau Imagerie-Genotoul ( TRI-Genotoul), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ANR-21-CE42-0018,TeraCellATR,Capteur térahertz ATR pour l'étude en temps réel de la perméabilisation des membranes cellulaires(2021), and 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)
Subjects: General Chemical Engineering, [SPI.PLASMA]Engineering Sciences [physics]/Plasmas, General Engineering, General Physics and Astronomy, Medicine (miscellaneous), self-assembly, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, plasma membrane, Biochemistry, Genetics and Molecular Biology (miscellaneous), photodynamic therapy PDT, [PHYS.PHYS.PHYS-MED-PH]Physics [physics]/Physics [physics]/Medical Physics [physics.med-ph], General Materials Science, permeability, polymers
Abstract: International audience; Methods to follow in real time complex processes occurring along living cell membranes such as cell permeabilization are rare. Here, the terahertz spectroscopy reveals early events in plasma membrane alteration generated during photodynamic therapy (PDT) protocol, events which are not observable in any other conventional biological techniques performed in parallel as comparison. Photodynamic process is examined in Madin-Darby canine kidney cells using Pheophorbide (Pheo) photosensitizer alone or alternatively encapsulated in poly(ethylene oxide)-block-poly(ε-caprolactone) micelles for drug delivery purpose. Terahertz spectroscopy (THz) reveals that plasma membrane permeabilization starts simultaneously with illumination and is stronger when photosensitizer is encapsulated. In parallel, the exchange of biological species is assessed. Over several hours, this conventional approach demonstrates significant differences between free and encapsulated Pheo, the latter leading to high penetration of propidium iodide, Na+ and Ca2+ ions, and a high level of leakage of K+, ATP, and lactate dehydrogenase. THz spectroscopy provides, in a single measurement, the relative number of defects per membrane surface created after PDT, which is not achieved by any other method, providing early, sensitive real-time information. THz spectroscopy is therefore a promising technique and can be applied to any biological topic requiring the examination of short-term plasma membrane permeabilization.
Published: 2023

18. Guidelines for G-quadruplexes: I. In vitro characterization

Author: Yu Luo, Anton Granzhan, Julien Marquevielle, Anne Cucchiarini, Laurent Lacroix, Samir Amrane, Daniela Verga, Jean-Louis Mergny, Mergny, Jean-Louis, Role des G-quadruplexes dans la régulation transcriptionnelle - - G4Access2020 - ANR-20-CE12-0023 - AAPG2020 - VALID, Pertinence biologique et ciblage de l'ADN i-motif - - iCARE2021 - ANR-21-CE44-0005 - AAPG2021 - VALID, Laboratoire d'Optique et Biosciences (LOB), École polytechnique (X)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Chimie et modélisation pour la biologie du cancer (CMBC), Institut Curie [Paris]-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), Institut Européen de Chimie et Biologie (IECB), Université de Bordeaux (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Acides Nucléiques : Régulations Naturelle et Artificielle (ARNA), Université de Bordeaux (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie de l'ENS Paris (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institute of Biophysics of the Czech Academy of Sciences (IBP / CAS), Czech Academy of Sciences [Prague] (CAS), ANR-20-CE12-0023,G4Access,Role des G-quadruplexes dans la régulation transcriptionnelle(2020), and ANR-21-CE44-0005,iCARE,Pertinence biologique et ciblage de l'ADN i-motif(2021)
Subjects: [SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, [SDV.BBM.BP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, General Medicine, Biochemistry
Abstract: International audience; Besides the well-known DNA double-helix, non-canonical nucleic acid structures regulate crucial bio- logical activities. Among these oddities, guanine-rich DNA sequences can form unusual four-stranded secondary structures called G-quadruplexes (G4s). G4-prone sequences have been found in the ge- nomes of most species, and G4s play important roles in essential processes such as transcription, replication, genome integrity and epigenetic regulation. Here, we present a short overview of G-quad- ruplexes followed by a detailed description of the biophysical and biochemical methods used to char- acterize G4s in vitro. The principles, experimental details and possible shortcomings of each method are discussed to provide a comprehensive view of the techniques used to study these structures. We aim to provide a set of guidelines for standardizing research on G-quadruplexes; these guidelines are not meant to be a dogmatic set of rules, but should rather provide useful information on the methods currently used to study these fascinating motifs.
Published: 2022

19. A single cell transcriptomic and clonal analysis depicts valvulogenesis

Author: Farhat, Batoul, Bordeu, Ignacio, Jagla, Bernd, Blanc, Hugo, Livet, Jean, Simons, Benjamin, Beaurepaire, Emmanuel, Pucéat, Michel, Marseille medical genetics - Centre de génétique médicale de Marseille (MMG), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge [UK] (CAM), Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Optique et Biosciences (LOB), École polytechnique (X)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), 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), and Beaurepaire, Emmanuel
Subjects: [SDV] Life Sciences [q-bio], [SDV]Life Sciences [q-bio]
Abstract: Mitral valve prolapse is often associated with several congenital heart malformations. During development, endocardial cells of the atrioventricular canal undergo endothelial to mesenchymal transition (EndMT) to give rise to the different mitral valvular cells. However, our understanding of the identity and fate decisions of these endocardial cells during development is lacking. Here, using single-cell RNA sequencing (scRNA-seq) of genetically labeled AVC endocardial cells at E9.5 in murine heart, we uncovered and genetically characterized a restricted population of pro-EndMT cells and further distinct populations of valve progenitors that together contribute to different endothelial and interstitial valvular cells in E16.5 embryonic and P0 postnatal murine mitral valve. Moreover, by genetically labeling endocardial cells using CAG ERT2Cre+/- / Brainbow +/- mice at embryonic stage E8.5, prior to EndMT, we observed specific modes of growth of endocardial derived clones in E16.5 embryonic mitral valve. Collectively, our data reveal the identity of specified endocardial cells and the distinct types of clonal contribution of these cells to the formation of the mitral valve. They further open the path towards finding new cell targets for a therapeutic approach of congenital and acquired valve diseases.
Published: 2022

20. Gallic Acid-Triethylene Glycol Aptadendrimers Synthesis, Biophysical Characterization and Cellular Evaluation

Author: André Miranda, Roi Lopez-Blanco, Jéssica Lopes-Nunes, Ana M. Melo, Maria Paula Cabral Campello, António Paulo, Maria Cristina Oliveira, Jean-Louis Mergny, Paula A. Oliveira, Eduardo Fernandez-Megia, Carla Cruz, University of Beira Interior [Portugal] (UBI), Universidade de Santiago de Compostela [Spain] (USC ), Universidade de Lisboa, Laboratoire d'Optique et Biosciences (LOB), École polytechnique (X)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut Polytechnique de Paris (IP Paris), University of Trás-os-Montes and Alto Douro [Portugal] (UTAD), and Mergny, Jean-Louis
Subjects: [SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, biophysical studies, gallic acid–triethylene glycol dendrimers, acridine orange ligands, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, Pharmaceutical Science, [SDV.BBM.BP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, aptadendrimer, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, G-quadruplex aptamers, G-quadruplex aptamer, [SDV.BC] Life Sciences [q-bio]/Cellular Biology
Abstract: International audience; Herein, we describe the synthesis of an aptadendrimer by covalent bioconjugation of a gallic acid–triethylene glycol (GATG) dendrimer with the G-quadruplex (G4) AT11 aptamer (a modified version of AS1411) at the surface. We evaluated the loading and interaction of an acridine orange ligand, termed C8, that acts as an anticancer drug and binder/stabilizer of the G4 structure of AT11. Dynamic light scattering experiments demonstrated that the aptadendrimer was approximately 3.1 nm in diameter. Both steady-state and time-resolved fluorescence anisotropy evidenced the interaction between the aptadendrimer and C8. Additionally, we demonstrated that the iodine atom of the C8 ligand acts as an effective intramolecular quencher in solution, while upon complexation with the aptadendrimer, it adopts a more extended conformation. Docking studies support this conclusion. Release experiments show a delivery of C8 after 4 h. The aptadendrimers tend to localize in the cytoplasm of various cell lines studied as demonstrated by confocal microscopy. The internalization of the aptadendrimers is not nucleolin-mediated or by passive diffusion, but via endocytosis. MTT studies with prostate cancer cells and non-malignant cells evidenced high cytotoxicity mainly due to the C8 ligand. The rapid internalization of the aptadendrimers and the fluorescence properties make them attractive for the development of potential nanocarriers.
Published: 2022

21. Design, Synthesis, and Antiprotozoal Evaluation of New Promising 2,9-Bis[(substituted-aminomethyl)]-4,7-phenyl-1,10phenanthroline Derivatives, a Potential Alternative Scaffold to Drug Efflux

Author: Jean Guillon, Anita Cohen, Clotilde Boudot, Sarah Monic, Solène Savrimoutou, Stéphane Moreau, Sandra Albenque-Rubio, Camille Lafon-Schmaltz, Alexandra Dassonville-Klimpt, Jean-Louis Mergny, Luisa Ronga, Mikel Bernabeu de Maria, Jeremy Lamarche, Cristina Dal Lago, Eric Largy, Valérie Gabelica, Serge Moukha, Pascale Dozolme, Patrice Agnamey, Nadine Azas, Catherine Mullié, Bertrand Courtioux, Pascal Sonnet, Acides Nucléiques : Régulations Naturelle et Artificielle (ARNA), Université de Bordeaux (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées (IRBA), Neuroépidémiologie Tropicale (NET), CHU Limoges-Institut d'Epidémiologie Neurologique et de Neurologie Tropicale-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Génomique, Environnement, Immunité, Santé, Thérapeutique (GEIST), Université de Limoges (UNILIM)-Université de Limoges (UNILIM), Agents infectieux, résistance et chimiothérapie - UR UPJV 4294 (AGIR ), Université de Picardie Jules Verne (UPJV)-CHU Amiens-Picardie, Laboratoire d'Optique et Biosciences (LOB), École polytechnique (X)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut Polytechnique de Paris (IP Paris), Institut des sciences analytiques et de physico-chimie pour l'environnement et les materiaux (IPREM), Université de Pau et des Pays de l'Adour (UPPA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Environnement, Santé/Stic (E2S), Université de Bourgogne (UB), Université de Pau et des Pays de l'Adour (UPPA), Institut Européen de Chimie et Biologie (IECB), Université de Bordeaux (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre de recherche Cardio-Thoracique de Bordeaux [Bordeaux] (CRCTB), Université Bordeaux Segalen - Bordeaux 2-CHU Bordeaux [Bordeaux]-Institut National de la Santé et de la Recherche Médicale (INSERM), Mergny, Jean-Louis, Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), Unité de recherche Mycologie et Sécurité des Aliments (MycSA), and Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: Microbiology (medical), General Immunology and Microbiology, G-quadruplex, antimalarial activity, phenanthroline, antileishmanial activity, antitrypanosomal activity, [SDV.BBM.BP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, [SDV.BC.BC]Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC], [SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, Infectious Diseases, [SDV.BC.BC] Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC], Immunology and Allergy, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], Molecular Biology, [SDV.BBM.BC] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM]
Abstract: International audience; A series of novel 2,9-bis[(substituted-aminomethyl)]-4,7-phenyl-1,10-phenanthroline derivatives was designed, synthesized, and evaluated in vitro against three protozoan parasites (Plasmodium falciparum, Leishmania donovani and Trypanosoma brucei brucei). Pharmacological results showed antiprotozoal activity with IC50 values in the sub and μM range. In addition, the in vitro cytotoxicity of these original molecules was assessed with human HepG2 cells. The substituted diphenylphenanthroline 1l was identified as the most potent antimalarial derivative with a ratio of cytotoxic to antiparasitic activities of 505.7 against the P. falciparum CQ-resistant strain W2. Against the promastigote forms of L. donovani, the phenanthrolines 1h, 1j, 1n and 1o were the most active with IC50 from 2.52 to 4.50 μM. The phenanthroline derivative 1o was also identified as the most potent trypanosomal candidate with a selectivity index (SI) of 91 on T. brucei brucei strain. FRET melting and native mass spectrometry experiments evidenced that the nitrogen heterocyclic derivatives bind the telomeric G-quadruplexes of P. falciparum and Trypanosoma. Moreover, as the telomeres of the parasites P. falciparum and Trypanosoma could be considered to be possible targets of this kind of nitrogen heterocyclic derivatives, their potential ability to stabilize the parasitic telomeric G-quadruplexes have been determined through the FRET melting assay and by native mass spectrometry.
Published: 2022

22. Synthesis and evaluation of 2,9-disubstituted-1,10-phenanthroline derivatives as G-quadruplex binders

Author: Joana Figueiredo, Israel Carreira-Barral, Roberto Quesada, Jean-Louis Mergny, Carla Cruz, University of Beira Interior [Portugal] (UBI), Universidad de Burgos, Laboratoire d'Optique et Biosciences (LOB), École polytechnique (X)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institute of Biophysics of the Czech Academy of Sciences (IBP / CAS), Czech Academy of Sciences [Prague] (CAS), and Mergny, Jean-Louis
Subjects: Guanine, Circular Dichroism, In vitro studies, Organic Chemistry, Clinical Biochemistry, Pharmaceutical Science, DNA, Telomere, Ligands, Biochemistry, 10-phenanthroline derivatives, G-Quadruplexes, Biophysical evaluation, Drug Discovery, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, Humans, RNA, Molecular Medicine, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, G-quadruplex structures, Molecular Biology, Phenanthrolines, 9-disubstituted-1
Abstract: International audience; G-quadruplex (G4) structures are non-canonical DNA/RNA secondary structures able to form within guanine rich nucleic acids sequences. They are present in several regions of the human genome including gene promoters, untranslated sequences, and telomeres. Due to their biological relevance G4 structures are considered important drug targets, in particular for anticancer therapies, leading to the development of G4 stabilizing small molecules. Telomeric regions have received special attention in this field since they can fold into several distinct intramolecular G-quadruplexes topologies. Herein, we report the synthesis of 2,9-disubstituted-1,10-phenanthroline derivatives and their ability to stabilize different intramolecular telomeric G4 sequences. We evaluated ligand-induced stabilization, selectivity and specificity of ligands using Förster Resonance Energy Transfer (FRET) melting experiments and circular dichroism (CD). In addition, we assessed the cytotoxicity of ligands against two cancer cell lines (A549 and H1299) and one healthy cell line (NHDF).
Published: 2022

23. Determination of collagen fibril size via absolute measurements of second-harmonic generation signals

Author: Thibaud Coradin, Marie-Claire Schanne-Klein, Stéphane Bancelin, Laura Kowalczuk, Carole Aimé, Ivan Gusachenko, Gaël Latour, Laboratoire d'optique et biosciences (LOB), École polytechnique (X)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Matériaux et Biologie (MATBIO), Laboratoire de Chimie de la Matière Condensée de Paris (LCMCP), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Collège de France (CdF (institution))-Institut de Chimie du CNRS (INC)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Collège de France (CdF (institution))-Institut de Chimie du CNRS (INC), Centre de Recherche des Cordeliers (CRC (UMR_S 872)), Université Paris Descartes - Paris 5 (UPD5)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'optique et biosciences ( LOB ), École polytechnique ( X ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Matériaux et Biologie ( MATBIO ), Laboratoire de Chimie de la Matière Condensée de Paris ( LCMCP ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Collège de France ( CdF ) -Centre National de la Recherche Scientifique ( CNRS ) -Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Collège de France ( CdF ) -Centre National de la Recherche Scientifique ( CNRS ), Centre de Recherche des Cordeliers ( CRC (UMR_S 872) ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Université Paris Descartes - Paris 5 ( UPD5 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Université Pierre et Marie Curie - Paris 6 (UPMC)-Collège de France (CdF (institution))-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Collège de France (CdF (institution))-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), and Roura, Denis
Subjects: Tail, [PHYS.PHYS.PHYS-OPTICS] Physics [physics]/Physics [physics]/Optics [physics.optics], Materials science, [SDV.IB.IMA]Life Sciences [q-bio]/Bioengineering/Imaging, [PHYS.PHYS.PHYS-BIO-PH]Physics [physics]/Physics [physics]/Biological Physics [physics.bio-ph], General Physics and Astronomy, Nanotechnology, 02 engineering and technology, Fibril, Signal, Collagen Type I, General Biochemistry, Genetics and Molecular Biology, Diabetes Mellitus, Experimental, Extracellular matrix, 03 medical and health sciences, [ PHYS.PHYS.PHYS-BIO-PH ] Physics [physics]/Physics [physics]/Biological Physics [physics.bio-ph], Cornea, Microscopy, Image Processing, Computer-Assisted, medicine, Animals, Descemet Membrane, [ SDV.IB.IMA ] Life Sciences [q-bio]/Bioengineering/Imaging, 030304 developmental biology, 0303 health sciences, [PHYS.PHYS.PHYS-OPTICS]Physics [physics]/Physics [physics]/Optics [physics.optics], Multidisciplinary, [ PHYS.PHYS.PHYS-OPTICS ] Physics [physics]/Physics [physics]/Optics [physics.optics], [PHYS.PHYS.PHYS-BIO-PH] Physics [physics]/Physics [physics]/Biological Physics [physics.bio-ph], Second-harmonic generation, General Chemistry, 021001 nanoscience & nanotechnology, Extracellular Matrix, Rats, Microscopy, Electron, [SDV.IB.IMA] Life Sciences [q-bio]/Bioengineering/Imaging, Membrane, medicine.anatomical_structure, Biophysics, 0210 nano-technology, Triple helix
Abstract: International audience; The quantification of collagen fibril size is a major issue for the investigation of pathological disorders associated with structural defects of the extracellular matrix. Second-harmonic generation microscopy is a powerful technique to characterize the macromolecular organization of collagen in unstained biological tissues. Nevertheless, due to the complex coherent building of this nonlinear optical signal, it has never been used to measure fibril diameter so far. Here we report absolute measurements of second-harmonic signals from isolated fibrils down to 30 nm diameter, via implementation of correlative second-harmonic-electron microscopy. Moreover, using analytical and numerical calculations, we demonstrate that the high sensitivity of this technique originates from the parallel alignment of collagen triple helices within fibrils and the subsequent constructive interferences of second-harmonic radiations. Finally, we use these absolute measurements as a calibration for ex vivo quantification of fibril diameter in the Descemet's membrane of a diabetic rat cornea.
Published: 2014

24. G-Quadruplex Aptamer-Ligand Characterization

Author: David Moreira, Daniela Leitão, Jéssica Lopes-Nunes, Tiago Santos, Joana Figueiredo, André Miranda, Daniela Alexandre, Cândida Tomaz, Jean-Louis Mergny, Carla Cruz, University of Beira Interior [Portugal] (UBI), Laboratoire d'Optique et Biosciences (LOB), École polytechnique (X)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut Polytechnique de Paris (IP Paris), Institute of Biophysics of the Czech Academy of Sciences (IBP / CAS), Czech Academy of Sciences [Prague] (CAS), and Mergny, Jean-Louis
Subjects: ligands, [SDV]Life Sciences [q-bio], G-quadruplex aptamer, aptamer–ligand interactions, biophysical techniques, Organic Chemistry, Pharmaceutical Science, Aptamers, Nucleotide, Tongue Neoplasms, Analytical Chemistry, G-Quadruplexes, [SDV] Life Sciences [q-bio], Chemistry (miscellaneous), Drug Discovery, Carcinoma, Squamous Cell, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, Humans, Molecular Medicine, aptamer-ligand interactions, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Physical and Theoretical Chemistry
Abstract: International audience; In this work we explore the structure of a G-rich DNA aptamer termed AT11-L2 (TGGTGGTGGTTGTTGTTGGTGGTGGTGGT; derivative of AT11) by evaluating the formation and stability of G-quadruplex (G4) conformation under different experimental conditions such as KCl concentration, temperature, and upon binding with a variety of G4 ligands (360A, BRACO-19, PDS, PhenDC3, TMPyP4). We also determined whether nucleolin (NCL) can be a target of AT11-L2 G4. Firstly, we assessed by circular dichroism, UV and NMR spectroscopies the formation of G4 by AT11-L2. We observed that, for KCl concentrations of 65 mM or less, AT11-L2 adopts hybrid or multiple topologies. In contrast, a parallel topology predominates for buffer containing 100 mM of KCl. The Tm of AT11-L2 in 100 mM of KCl is 38.9 °C, proving the weak stability of this sequence. We also found that upon titration with two molar equivalents of 360A, BRACO-19 and PhenDC3, the G4 is strongly stabilized and its topology is maintained, while the addition of 3.5 molar equivalents of TMPyP4 promotes the disruption of G4. The KD values between AT11-L2 G4, ligands and NCL were obtained by fluorescence titrations and are in the range of µM for ligand complexes and nM when adding NCL. In silico studies suggest that four ligands bind to the AT11-L2 G4 structure by stacking interactions, while the RBD1,2 domains of NCL interact preferentially with the thymines of AT11-L2 G4. Finally, AT11-L2 G4 co-localized with NCL in NCL-positive tongue squamous cell carcinoma cell line.
Published: 2022
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25. Sol-gel transition induced by alumina nanoparticles in a model pulmonary surfactant

Author: Jean-François Berret, Fanny Mousseau, Rémi Le Borgne, Evdokia K. Oikonomou, Matière et Systèmes Complexes (MSC (UMR_7057)), Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Laboratoire d'Optique et Biosciences (LOB), École polytechnique (X)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut Jacques Monod (IJM (UMR_7592)), and Université Paris Cité, Equipe HAL
Subjects: Curosurf®, [SPI]Engineering Sciences [physics], Colloid and Surface Chemistry, [SPI] Engineering Sciences [physics], Soft Condensed Matter (cond-mat.soft), FOS: Physical sciences, Pulmonary surfactant, Bio-nano interfaces, Condensed Matter - Soft Condensed Matter, Microrheology, Magnetic wires
Abstract: Inhaled airborne particles smaller than 100 nm entering the airways have been shown to deposit in significant amount in the alveolar region of the lungs. The interior of the alveoli is covered with a ~ 1 micron thick lining fluid, called pulmonary surfactant. Inhaled nanoparticles are susceptible to interact with the lung fluid and modify pulmonary functions. Here we evaluate the structural and rheological properties of the pulmonary surfactant substitute Curosurf which is administered to premature babies for the treatment of respiratory distress syndrome. Curosurf is considered a reliable model of endogenous pulmonary surfactant in terms of composition, structure and function. Using active microrheology based on magnetically actuated wires, we find that Curosurf dispersions exhibit a Newtonian behavior at lipid concentration from 0 to 80 g L-1, and that the viscosity follows the Krieger-Dougherty law observed for a wide variety of colloids. Upon addition of 40 nm alumina nanoplatelets, a significant change of the Curosurf rheology is noticed. The dispersions then enter a soft solid phase characterized by an infinite viscosity and a non-zero equilibrium elastic modulus. The sol-gel transition induced by the nanoparticles is interpreted as the result of the alumina/vesicle interaction, which are illustrated by transmission electron microscopy. It also suggests a potential toxicity associated with the modification of the lung fluid structural and dynamical properties., Comment: 15 pages, 5 figures, 38 references
Published: 2022

26. Multimodal Highlighting of Structural Abnormalities in Diabetic Rat and Human Corneas

Author: Michèle Savoldelli, Francine Behar-Cohen, Gaël Latour, Jean-Claude Jeanny, Laura Kowalczuk, Marie-Claire Schanne-Klein, Jean-Louis Bourges, Karsten Plamann, Laboratoire d'optique appliquée (LOA), École Nationale Supérieure de Techniques Avancées (ENSTA Paris)-École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS), Centre de Recherche des Cordeliers (CRC (UMR_S 872)), Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Service d'ophtalmologie [Hôtel-Dieu - Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôtel-Dieu, Laboratoire d'optique et biosciences (LOB), École polytechnique (X)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'optique appliquée ( LOA ), École Nationale Supérieure de Techniques Avancées ( Univ. Paris-Saclay, ENSTA ParisTech ) -École polytechnique ( X ) -Centre National de la Recherche Scientifique ( CNRS ), Centre de Recherche des Cordeliers ( CRC (UMR_S 872) ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Université Paris Descartes - Paris 5 ( UPD5 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Assistance publique - Hôpitaux de Paris (AP-HP)-Hôtel-Dieu, Laboratoire d'optique et biosciences ( LOB ), École polytechnique ( X ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), and Roura, Denis
Subjects: [PHYS.PHYS.PHYS-OPTICS] Physics [physics]/Physics [physics]/Optics [physics.optics], Pathology, medicine.medical_specialty, [SDV.IB.IMA]Life Sciences [q-bio]/Bioengineering/Imaging, Biomedical Engineering, Article, law.invention, Extracellular matrix, 03 medical and health sciences, 0302 clinical medicine, Confocal microscopy, law, In vivo, Cornea, medicine, [ SDV.IB.IMA ] Life Sciences [q-bio]/Bioengineering/Imaging, 030304 developmental biology, Basement membrane, 0303 health sciences, [PHYS.PHYS.PHYS-OPTICS]Physics [physics]/Physics [physics]/Optics [physics.optics], [ PHYS.PHYS.PHYS-OPTICS ] Physics [physics]/Physics [physics]/Optics [physics.optics], business.industry, Histology, Epithelium, 3. Good health, Ophthalmology, [SDV.IB.IMA] Life Sciences [q-bio]/Bioengineering/Imaging, medicine.anatomical_structure, 030221 ophthalmology & optometry, Ultrastructure, sense organs, business
Abstract: International audience; PURPOSE: This study aimed to highlight structural corneal changes in a model of type 2 diabetes, using in vivo corneal confocal microscopy (CCM). The abnormalities were also characterized by transmission electron microscopy (TEM) and second harmonic generation (SHG) microscopy in rat and human corneas. METHODS: Goto-Kakizaki (GK) rats were observed at age 12 weeks (n = 3) and 1 year (n = 6), and compared to age-matched controls. After in vivo CCM examination, TEM and SHG microscopy were used to characterize the ultrastructure and the three-dimensional organization of the abnormalities. Human corneas from diabetic (n = 3) and nondiabetic (n = 3) patients were also included in the study. RESULTS: In the basal epithelium of GK rats, CCM revealed focal hyper-reflective areas, and histology showed proliferative cells with irregular basement membrane. In the anterior stroma, extracellular matrix modifications were detected by CCM and confirmed in histology. In the Descemet's membrane periphery of all the diabetic corneas, hyper-reflective deposits were highlighted using CCM and characterized as long-spacing collagen fibrils by TEM. SHG microscopy revealed these deposits with high contrast, allowing specific detection in diabetic human and rat corneas without preparation and characterization of their three-dimensional organization. CONCLUSION: Pathologic findings were observed early in the development of diabetes in GK rats. Similar abnormalities have been found in corneas from diabetic patients. TRANSLATIONAL RELEVANCE: This multidisciplinary study highlights diabetes-induced corneal abnormalities in an animal model, but also in diabetic donors. This could constitute a potential early marker for diagnosis of hyperglycemia-induced tissue changes.
Published: 2013

27. Hyperglycemia-induced abnormalities in rat and human corneas: the potential of second harmonic generation microscopy

Author: Michèle Savoldelli, Francine Behar-Cohen, Laura Kowalczuk, Gaël Latour, Marie-Claire Schanne-Klein, Jean-Louis Bourges, Karsten Plamann, Laboratoire d'optique et biosciences (LOB), École polytechnique (X)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre de Recherche des Cordeliers (CRC (UMR_S 872)), Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Service d'opthalmologie, Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Hôtel-Dieu [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Laboratoire d'optique appliquée (LOA), École Nationale Supérieure de Techniques Avancées (ENSTA Paris)-École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS), Physiopathologie des Maladies Oculaires : Innovations Therapeutiques, Université Pierre et Marie Curie - Paris 6 (UPMC)-IFR58-Institut National de la Santé et de la Recherche Médicale (INSERM), Lachapelle, Laure, Laboratoire d'optique et biosciences ( LOB ), École polytechnique ( X ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Centre de Recherche des Cordeliers ( CRC (UMR_S 872) ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Université Paris Descartes - Paris 5 ( UPD5 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Assistance publique - Hôpitaux de Paris (AP-HP)-Hôpital Hôtel-Dieu [Paris], Laboratoire d'optique appliquée ( LOA ), École Nationale Supérieure de Techniques Avancées ( Univ. Paris-Saclay, ENSTA ParisTech ) -École polytechnique ( X ) -Centre National de la Recherche Scientifique ( CNRS ), and Université Pierre et Marie Curie - Paris 6 ( UPMC ) -IFR58-Institut National de la Santé et de la Recherche Médicale ( INSERM )
Subjects: Male, Pathology, [SDV.IB.IMA]Life Sciences [q-bio]/Bioengineering/Imaging, Image Processing, Biochemistry, 01 natural sciences, law.invention, Cornea, Engineering, 0302 clinical medicine, law, Microscopy, Condensed-Matter Physics, [ SDV.IB.IMA ] Life Sciences [q-bio]/Bioengineering/Imaging, Aged, 80 and over, Extracellular Matrix Proteins, [PHYS.PHYS.PHYS-OPTICS]Physics [physics]/Physics [physics]/Optics [physics.optics], [ PHYS.PHYS.PHYS-OPTICS ] Physics [physics]/Physics [physics]/Optics [physics.optics], Microscopy, Confocal, Multidisciplinary, Physics, Animal Models, Diabetic retinopathy, Anatomy, Middle Aged, Second Harmonic Generation Microscopy, 3. Good health, medicine.anatomical_structure, [SDV.MHEP.OS] Life Sciences [q-bio]/Human health and pathology/Sensory Organs, [ SDV.MHEP.OS ] Life Sciences [q-bio]/Human health and pathology/Sensory Organs, Corneal Disorders, Medicine, Female, Preclinical imaging, Research Article, [PHYS.PHYS.PHYS-OPTICS] Physics [physics]/Physics [physics]/Optics [physics.optics], medicine.medical_specialty, animal structures, Science, Biophysics, 010309 optics, 03 medical and health sciences, Model Organisms, Imaging, Three-Dimensional, Optical imaging, Confocal microscopy, 0103 physical sciences, medicine, Animals, Humans, Rats, Wistar, [SDV.MHEP.OS]Life Sciences [q-bio]/Human health and pathology/Sensory Organs, Biology, Descemet Membrane, Aged, Chemical Physics, business.industry, Proteins, Second-harmonic generation, Optics, medicine.disease, eye diseases, Rats, Ophthalmology, [SDV.IB.IMA] Life Sciences [q-bio]/Bioengineering/Imaging, Cornea/abnormalities, Cornea/pathology, Descemet Membrane/abnormalities, Descemet Membrane/pathology, Diabetes Mellitus, Type 2/pathology, Hyperglycemia/pathology, Microscopy/methods, Diabetes Mellitus, Type 2, Hyperglycemia, Signal Processing, 030221 ophthalmology & optometry, Rat, sense organs, business
Abstract: International audience; BACKGROUND: Second Harmonic Generation (SHG) microscopy recently appeared as an efficient optical imaging technique to probe unstained collagen-rich tissues like cornea. Moreover, corneal remodeling occurs in many diseases and precise characterization requires overcoming the limitations of conventional techniques. In this work, we focus on diabetes, which affects hundreds of million people worldwide and most often leads to diabetic retinopathy, with no early diagnostic tool. This study then aims to establish the potential of SHG microscopy for in situ detection and characterization of hyperglycemia-induced abnormalities in the Descemet's membrane, in the posterior cornea. METHODOLOGY/PRINCIPAL FINDINGS: We studied corneas from age-matched control and Goto-Kakizaki rats, a spontaneous model of type 2 diabetes, and corneas from human donors with type 2 diabetes and without any diabetes. SHG imaging was compared to confocal microscopy, to histology characterization using conventional staining and transmitted light microscopy and to transmission electron microscopy. SHG imaging revealed collagen deposits in the Descemet's membrane of unstained corneas in a unique way compared to these gold standard techniques in ophthalmology. It provided background-free images of the three-dimensional interwoven distribution of the collagen deposits, with improved contrast compared to confocal microscopy. It also provided structural capability in intact corneas because of its high specificity to fibrillar collagen, with substantially larger field of view than transmission electron microscopy. Moreover, in vivo SHG imaging was demonstrated in Goto-Kakizaki rats. CONCLUSIONS/SIGNIFICANCE: Our study shows unambiguously the high potential of SHG microscopy for three-dimensional characterization of structural abnormalities in unstained corneas. Furthermore, our demonstration of in vivo SHG imaging opens the way to long-term dynamical studies. This method should be easily generalized to other structural remodeling of the cornea and SHG microscopy should prove to be invaluable for in vivo corneal pathological studies.
Published: 2012

28. Table-top resonant magnetic scattering with extreme ultraviolet light from high-order harmonic generation

Author: Christine Boeglin, Stéphane Sebban, Jan Lüning, Jacek Arabski, Eric Beaurepaire, Evgueni Meltchakov, M. Lozano, Franck Delmotte, Boris Vodungbo, Julien Gautier, Renaud Delaunay, A. Barszczak Sardinha, Guillaume Lambert, Philippe Zeitoun, Victor Lopez-Flores, Laboratoire d'optique appliquée (LOA), École Nationale Supérieure de Techniques Avancées (ENSTA Paris)-École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS), Centre de Recherche des Cordeliers (CRC), Université Paris Diderot - Paris 7 (UPD7)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratoire de Sociologie et d'Anthropologie - UFC (EA 3189) (LASA), Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Laboratoire Charles Fabry de l'Institut d'Optique / Scop, Laboratoire Charles Fabry de l'Institut d'Optique (LCFIO), Université Paris-Sud - Paris 11 (UP11)-Institut d'Optique Graduate School (IOGS)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Sud - Paris 11 (UP11)-Institut d'Optique Graduate School (IOGS)-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 d'Alsace, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Université de Strasbourg (UNISTRA)-Réseau nanophotonique et optique, Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Université de Strasbourg (UNISTRA), Laboratoire d'optique et biosciences (LOB), École polytechnique (X)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Chimie Physique - Matière et Rayonnement (LCPMR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'optique appliquée ( LOA ), École Nationale Supérieure de Techniques Avancées ( Univ. Paris-Saclay, ENSTA ParisTech ) -École polytechnique ( X ) -Centre National de la Recherche Scientifique ( CNRS ), Centre de Recherche des Cordeliers ( CRC ), Université Paris Diderot - Paris 7 ( UPD7 ) -École pratique des hautes études ( EPHE ) -Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Université Paris Descartes - Paris 5 ( UPD5 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ), Laboratoire de Sociologie et d'Anthropologie - UFC (EA 3189) ( LASA ), Université Bourgogne Franche-Comté [COMUE] ( UBFC ) -Université de Franche-Comté ( UFC ), Laboratoire Charles Fabry de l'Institut d'Optique ( LCFIO ), Université Paris-Sud - Paris 11 ( UP11 ) -Institut d'Optique Graduate School ( IOGS ) -Centre National de la Recherche Scientifique ( CNRS ) -Université Paris-Sud - Paris 11 ( UP11 ) -Institut d'Optique Graduate School ( IOGS ) -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 d'Alsace, 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 ) -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 ) -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 ), Laboratoire d'optique et biosciences ( LOB ), École polytechnique ( X ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de Chimie Physique - Matière et Rayonnement ( LCPMR ), Centre National de la Recherche Scientifique ( CNRS ) -Université Pierre et Marie Curie - Paris 6 ( UPMC ), Centre National de la Recherche Scientifique (CNRS)-Institut d'Optique Graduate School (IOGS)-Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS)-Institut d'Optique Graduate School (IOGS)-Université Paris-Sud - Paris 11 (UP11), Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université Pierre et Marie Curie - Paris 6 (UPMC), Centre National de la Recherche Scientifique (CNRS)-École polytechnique (X)-École Nationale Supérieure de Techniques Avancées (ENSTA Paris), Université Paris Diderot - Paris 7 (UPD7)-École pratique des hautes études (EPHE)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université de Franche-Comté (UFC), 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)-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)-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), Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Université Paris Descartes - Paris 5 ( UPD5 ) -Université Pierre et Marie Curie - Paris 6 ( UPMC ) -École pratique des hautes études ( EPHE ) -Université Paris Diderot - Paris 7 ( UPD7 ), Laboratoire de Sociologie et d'Anthropologie - UFC ( LASA ), Université Bourgogne Franche-Comté ( UBFC ) -Université de Franche-Comté ( UFC ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Centre National de la Recherche Scientifique ( CNRS ), Grupo de Lasers e Plasmas, Instituto Superior Tcnico, 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), and Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Magnetic domain, [PHYS.PHYS.PHYS-ACC-PH]Physics [physics]/Physics [physics]/Accelerator Physics [physics.acc-ph], Aucun, General Physics and Astronomy, 02 engineering and technology, 01 natural sciences, law.invention, Optics, law, [PHYS.PHYS.PHYS-PLASM-PH]Physics [physics]/Physics [physics]/Plasma Physics [physics.plasm-ph], 0103 physical sciences, High harmonic generation, [ PHYS.PHYS.PHYS-ACC-PH ] Physics [physics]/Physics [physics]/Accelerator Physics [physics.acc-ph], 010306 general physics, Physics, [PHYS]Physics [physics], Magnetization dynamics, [PHYS.PHYS.PHYS-OPTICS]Physics [physics]/Physics [physics]/Optics [physics.optics], [ PHYS ] Physics [physics], [ PHYS.PHYS.PHYS-OPTICS ] Physics [physics]/Physics [physics]/Optics [physics.optics], business.industry, Scattering, [ PHYS.PHYS.PHYS-PLASM-PH ] Physics [physics]/Physics [physics]/Plasma Physics [physics.plasm-ph], 021001 nanoscience & nanotechnology, Laser, [PHYS.COND.CM-GEN]Physics [physics]/Condensed Matter [cond-mat]/Other [cond-mat.other], Extreme ultraviolet, Femtosecond, Optoelectronics, 0210 nano-technology, business, Ultrashort pulse
Abstract: We demonstrate for the first time the applicability of high-order harmonic generation for probing magnetization properties with nanometer spatial resolution. High harmonics were generated by focusing an infrared femtosecond laser into a neon-filled gas cell. Using a high throughput monochromator, EUV pulses with a photon energy resonant to the magnetically dichroic Co M(2,3) absorption resonance were obtained. These were focused onto a CoPd alloy film and the magnetic scattering pattern was recorded in a transmission geometry. The scattering pattern induced by the magnetic domain structure consists of two well-defined bright spots revealing the presence of stripe domains of about 63nm in width. With the inherent femtosecond time resolution given by high harmonics, this demonstration paves the way to investigate ultrafast magnetization dynamics with femtosecond time and nanometer spatial resolutions, in jitter-free experiment based on table-top EUV light sources. Copyright (C) EPLA, 2011
Published: 2011

29. Impact of pulse polarization on coherent vibrational ladder climbing signals

Author: Patrick Nuernberger, Manuel Joffre, Thibault Vieille, Cathie Ventalon, Laboratoire d'optique et biosciences (LOB), École polytechnique (X)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut für Physikalische und Theoretische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, affiliation inconnue, FASTLITE, Centre Scientifique d'Orsay, Bât. 503, 91401 Orsay, Laboratoire de Neurophysiologie et Nouvelles Microscopies (U1128), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratoire d'optique et biosciences ( LOB ), École polytechnique ( X ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de Neurophysiologie et Nouvelles Microscopies ( U1128 ), and Université Paris Descartes - Paris 5 ( UPD5 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM )
Subjects: education.field_of_study, Chemistry, business.industry, Attenuation, Population, Probability density function, 010402 general chemistry, Polarization (waves), 01 natural sciences, 0104 chemical sciences, Surfaces, Coatings and Films, Optics, Excited state, Climbing, 0103 physical sciences, Ultrafast laser spectroscopy, Materials Chemistry, Physical and Theoretical Chemistry, Atomic physics, 010306 general physics, business, education, Ultrashort pulse
Abstract: International audience; We report a theoretical study that elaborates the influence of the polarization state of both the pump and the probe pulse in ultrafast coherent vibrational ladder climbing experiments in the mid-infrared. Whereas a subensemble in a randomly oriented sample of molecules is excited by the pump pulse in this multiphoton process, further inhomogeneities such as the spatial profile of the laser beams, the longitudinal attenuation in the sample, and the probe beam polarization have to be taken into account. Analytical expressions for a density function describing the number of molecules that are exposed to an effective pump intensity are introduced, and the variation of the population distribution and the actual transient absorption signal in dependence on the polarization-state combinations for pump and probe pulse are discussed in detail. In simulations on the model system carboxy-hemoglobin, it is demonstrated that the polarization states play important roles both for exciting a certain population distribution and for actually observing it. In particular, it will be discussed under which conditions experimental data indicates a population inversion. Cop. 2011 American Chemical Society.
Published: 2011

30. Fundamental Processes in Flavoprotein Photochemistry

Author: Zhuang, Bo, Laboratoire d'Optique et Biosciences (LOB), École polytechnique (X)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut Polytechnique de Paris, Marten H. Vos, Alexey Alexandrov, and STAR, ABES
Subjects: Flavoproteins, [PHYS.PHYS.PHYS-BIO-PH] Physics [physics]/Physics [physics]/Biological Physics [physics.bio-ph], Photochemistry, Simulation numérique, [PHYS.PHYS.PHYS-BIO-PH]Physics [physics]/Physics [physics]/Biological Physics [physics.bio-ph], Photochimie, Spectroscopie optique resolue en temps, Computer simulation, Flavoprotéines, Time-Resolved optical spectroscopy
Abstract: Flavins are derivatives of vitamin B2 that form a highly versatile group of chromophores found in a large variety of enzymes and photoreceptor proteins. They can adopt three different redox states with various protonation states, leading to at least five physiologically relevant forms, with distinct electronic absorption spectra. Despite the diverse photophysical properties of the flavin cofactors, there are only very few natural photo-responsive flavoproteins. The vast majority of flavoproteins perform non-light-driven physiological functions (“non-photoactive”), although ultrafast, reversible photoinduced redox reactions between flavins and surrounding residues still widely occur in these systems, which can be viewed as photo-protective “self-quenching”. The past few decades have seen a blooming in the study of flavoproteins for their photocatalytic and photo-biotechnological applications. Moreover, a newly emerging approach in the development of novel photocatalysts from canonical “non-photoactive” flavoenzymes is making use of the photochemistry of reduced flavins instead of the oxidized resting state. Furthermore, practical implications of photochemistry of yet different flavin species are envisaged, but a basic understanding of their mechanisms is still required. In this thesis, applying ultrafast absorption and fluorescence spectroscopy combined with molecular simulations and quantum chemistry approaches, a variety of fundamental photochemical processes in flavoproteins is investigated. First the photoreduction of oxidized flavins was revisited in a flavoprotein, ferredoxin-NADP+ oxidoreductase (FNR), with closely packed reactant configurations, allowing ultrafast formation of intermediate radical pairs. Combining experimental and modeling techniques allowed a detailed assessment of the influence of the environment on the spectral properties of both the anionic flavin and the cationic amino acid (tyrosine or tryptophan) radicals. We further investigated the photochemistry of protein-bound flavin species in different chemical states that are largely unexplored in the literature. It is demonstrated that photooxidation of anionic flavin radicals, which act as reaction intermediates in many biochemical reactions, efficiently occurs within ~100 fs in several flavoprotein oxidases. This process, effectively the reverse of the well-known photoreduction of oxidized flavin may constitute a universal decay pathway. The excited-state properties of fully reduced flavins were studied in several FNR systems where they are involved as functional intermediates, and compared with those in solution. Valuable information concerning their electronic structures and the flavin flexibility was obtained and compared with atomic simulations, with important catalytic implications. Finally, an unprecedented photo-dissociation phenomenon was revealed for a non-covalent charge transfer complex of flavin and a inhibitor in the flavoenzyme monomeric sarcosine oxidase. This process occurs on the timescale of a few hundred femtoseconds and can be attributed to a well-defined photoinduced isomerization of the inhibitor. Altogether, the described findings, which include the discovery of two hitherto undocumented photochemical processes in flavoproteins, expand the repertoire of photochemistry involving flavin cofactors. This work may open new avenues for the exploration of flavin photochemistry with ultimately possible practical implications as novel photocatalysts and optogenetic tools., Les flavines sont des dérivés de la vitamine B2 qui forment un groupe de chromophores très polyvalents présents dans une grande variété d'enzymes et de protéines photoréceptrices. Elles peuvent adopter trois états redox différents avec divers états de protonation, menant à au moins cinq formes physiologiquement pertinentes, avec des spectres d'absorption électronique distincts. Malgré les propriétés photophysiques diverses des cofacteurs flavine, il n'y a que très peu de flavoprotéines naturellement photoréactives. La grande majorité des flavoprotéines remplissent des fonctions physiologiques non générées par la lumière ("non-photoactives"), bien que des réactions d'oxydoréduction photo-induites ultra-rapides et réversibles entre les flavines et les résidus proches s’y produisent largement, ce qui peut être considéré comme "auto-quenching" photo-protectrice. Ces dernières décennies, l'étude des flavoprotéines a connu un essor pour leurs applications photocatalytiques et photo-biotechnologiques. De plus, une nouvelle approche émergeant dans le développement de nouveaux photocatalyseurs à partir de flavoenzymes canoniques "non-photoactives" utilise la photochimie de flavines réduites au lieu de l'état de repos oxydé. En outre, des implications pratiques de la photochimie d'espèces de flavine encore différentes sont envisagées, mais une compréhension fondamentale de leurs mécanismes est requise. Dans cette thèse, par l'application de spectroscopie d'absorption et de fluorescence ultrarapide combinée avec des simulations moléculaires et d’approches de chimie quantique, une variété de processus photochimiques fondamentaux dans les flavoprotéines est étudiée. Tout d'abord, la photoréduction des flavines oxydées a été revisitée dans une flavoprotéine, la ferrédoxine-NADP+ oxydoréductase (FNR), ayant des configurations des réactifs très compactes, permettant la formation ultrarapide de paires de radicaux intermédiaires. La combinaison de techniques expérimentales et de modélisation a permis une évaluation détaillée de l'influence de l'environnement sur les propriétés spectrales des radicaux anioniques de flavine et cationiques d'acide aminé (tyrosine ou tryptophane). Par ailleurs, nous avons étudié la photochimie de flavines liées aux protéines dans différents états chimiques largement inexplorés dans la littérature. Il est démontré que la photooxydation des radicaux anioniques de flavine, qui agissent comme des intermédiaires de réaction dans de nombreuses réactions biochimiques, se produit efficacement en ~100 fs dans plusieurs flavoprotéines oxydases. Ce processus, qui est effectivement l'inverse de la photoréduction bien connue de la flavine oxydée, pourrait constituer une voie de désactivation universelle. Les propriétés de l'état excité des flavines complétement réduites ont été étudiées dans plusieurs systèmes FNR où elles sont impliquées comme intermédiaires fonctionnels, et comparées à celles en solution. Des informations précieuses concernant leurs structures électroniques et la flexibilité des flavines ont été obtenues et comparées avec des simulations atomiques, avec des implications catalytiques importantes. Enfin, un phénomène de photo-dissociation sans précédent a été révélé pour un complexe de transfert de charge non covalent de la flavine et d'un inhibiteur dans la flavoenzyme sarcosine oxydase monomérique. Ce processus se produit sur une échelle de temps de quelques centaines de femtosecondes et peut être attribué à une isomérisation photoinduite bien définie de l'inhibiteur. Dans l'ensemble, les résultats décrits, qui incluent la découverte de deux processus photochimiques jusqu'alors non documentés dans les flavoprotéines, élargissent le répertoire de la photochimie impliquant des cofacteurs de flavine. Ce travail peut ouvrir de nouvelles voies pour l'exploration de la photochimie des flavines avec, à terme, des implications pratiques possibles comme nouveaux photocatalyseurs et outils optogénétiques.
Published: 2022

31. An Efficient Biocatalytic System for Biosensing by Combining Metal-Organic Framework (MOF)-based Nanozymes and G-quadruplex (G4)-DNAzymes

Author: Xuanxiang Mao, Fangni He, Dehui Qiu, Shijiong Wei, Rengan Luo, Yun Chen, Xiaobo Zhang, Jianping Lei, David Monchaud, Jean-Louis Mergny, Huangxian Ju, Jun Zhou, Nanjing University (NJU), Institut de Chimie Moléculaire de l'Université de Bourgogne [Dijon] (ICMUB), Université de Bourgogne (UB)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Optique et Biosciences (LOB), École polytechnique (X)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Monchaud, David, Mergny, Jean-Louis, and Université Bourgogne Franche-Comté [COMUE] (UBFC)
Subjects: [SDV.BIO]Life Sciences [q-bio]/Biotechnology, [SDV.BBM.BP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, [CHIM.CATA] Chemical Sciences/Catalysis, Biosensing Techniques, DNA, Catalytic, [CHIM.CATA]Chemical Sciences/Catalysis, Analytical Chemistry, [SDV.BIO] Life Sciences [q-bio]/Biotechnology, [SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, G-Quadruplexes, Hemin, Humans, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], [SDV.BBM.BC] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], Metal-Organic Frameworks
Abstract: International audience; A high catalytic efficiency associated with a robust chemical structure are among the ultimate goals when developing new biocatalytic systems for biosensing applications. To get ever closer to these goals, we report here on a combination of metal-organic framework (MOF)-based nanozymes and a G-quadruplex (G4)-based catalytic system known as G4-DNAzyme. This approach aims at combining the advantages of both partners (chiefly, the robustness of the former and the modularity of the latter). To this end, we used MIL-53(Fe) MOF and linked it covalently to a G4-forming sequence (F3TC), itself covalently linked to its cofactor hemin. The resulting complex (referred to as MIL-53(Fe)/G4-hemin) exhibited exquisite peroxidase-mimicking oxidation activity and an excellent robustness (being stored in water for weeks). These properties were exploited to devise a new biosensing system based on a cascade of reactions catalyzed by the nanozyme (ABTS oxidation) and an enzyme, the alkaline phosphatase (or ALP, ascorbic acid 2-phosphate dephosphorylation). The product of the latter poisoning the former, we thus designed a biosensor for ALP (a marker of bone diseases and cancers), with a very low limit of detection (LOD, 0.02 U L-1), which is operative in human plasma samples.
Published: 2022

32. Stabilization of a DNA aptamer by ligand binding

Author: Tiago Santos, Jéssica Lopes-Nunes, Daniela Alexandre, André Miranda, Joana Figueiredo, Micael S. Silva, Jean-Louis Mergny, Carla Cruz, University of Beira Interior [Portugal] (UBI), Laboratoire d'Optique et Biosciences (LOB), École polytechnique (X)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), and Mergny, Jean-Louis
Subjects: [SDV]Life Sciences [q-bio], [SDV.CAN]Life Sciences [q-bio]/Cancer, General Medicine, Aptamers, Nucleotide, Ligands, Biochemistry, Tongue Neoplasms, G-Quadruplexes, [SDV] Life Sciences [q-bio], [SDV.CAN] Life Sciences [q-bio]/Cancer, Carcinoma, Squamous Cell, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, Humans, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology
Abstract: International audience; G-rich aptamers such as AS1411 are small oligonucleotides that present several benefits comparatively to monoclonal antibodies, since they are easier to manufacture and store, have small size and do not stimulate an immune response. We analyzed AT11-B1, a modified sequence of AT11 (itself a modified version of AS1411), in which one thymine was removed from the bulge region. We studied G-quadruplex (G4) formation/stabilization using PhenDC3, PDS, BRACO-19, TMPyP4 and 360A ligands by different biophysical techniques, namely circular dichroism (CD), Förster resonance energy transfer (FRET-melting) and nuclear magnetic resonance (NMR). The CD spectra showed that AT11-B1 adopts a predominant G4 of parallel topology when the buffer contains KCl or when ligands are added. PhenDC3 induced a ΔTm of 30 °C or more of the G4 structure as shown by CD- and FRET-melting experiments. The ligands demonstrate high affinity for AT11-B1 G4 and the NMR studies revealed that the AT11-B1 G4 involves four G-tetrad layers. The in silico studies suggest that all ligands bind AT11-B1 G4, namely, by stacking interactions, except PDS that may bind to the loop/groove interface. In addition, molecular dynamics simulations revealed that nucleolin (NCL) interacts with the AT11-B1 G4 structure through the RNA binding domain (RBD) 2 and the 12-residue linker between RBD1,2. Moreover, AT11-B1 G4 was internalized into a NCL-positive tongue squamous cell carcinoma cell line. In a nutshell, this study may help the identification of the ligands scaffolds to bind and stabilize AT11-B1, improving the targeting towards NCL that is overexpressed in cancer cells.
Published: 2022

33. Multimodal Nonlinear Imaging of the Human Cornea

Author: Nicolas Olivier, Marie-Claire Schanne-Klein, Jean-Marc Legeais, Florent Aptel, Ariane Deniset-Besseau, Emmanuel Beaurepaire, Karsten Plamann, Laboratoire d'optique appliquée (LOA), École Nationale Supérieure de Techniques Avancées (ENSTA Paris)-École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Biotechnologie et Œil, Université Paris Descartes - Paris 5 (UPD5)-Hôpital Hôtel-Dieu [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Service d'Ophtalmologie [Hôpital Edouard Herriot - HCL]], Hôpital Edouard Herriot [CHU - HCL], Hospices Civils de Lyon (HCL)-Hospices Civils de Lyon (HCL), Laboratoire d'optique et biosciences (LOB), École polytechnique (X)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-École polytechnique (X)-École Nationale Supérieure de Techniques Avancées (ENSTA Paris), Laboratoire d'optique appliquée ( LOA ), École Nationale Supérieure de Techniques Avancées ( Univ. Paris-Saclay, ENSTA ParisTech ) -École polytechnique ( X ) -Centre National de la Recherche Scientifique ( CNRS ), Université Paris Descartes - Paris 5 ( UPD5 ) -Hôpital Hôtel-Dieu [Paris], Hospices Civils de Lyon ( HCL ) -Hospices Civils de Lyon ( HCL ), Laboratoire d'optique et biosciences ( LOB ), and École polytechnique ( X ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS )
Subjects: Materials science, Microscope, genetic structures, Corneal Stroma, Glaucoma, Fluorescence Polarization, Eye Banks, 01 natural sciences, law.invention, Cornea, 010309 optics, 03 medical and health sciences, 0302 clinical medicine, Trabecular Meshwork, law, 0103 physical sciences, Microscopy, medicine, Humans, [PHYS.PHYS.PHYS-OPTICS]Physics [physics]/Physics [physics]/Optics [physics.optics], [ PHYS.PHYS.PHYS-OPTICS ] Physics [physics]/Physics [physics]/Optics [physics.optics], Corneal Edema, Endothelium, Corneal, Resolution (electron density), Epithelium, Corneal, Eye bank, Anatomy, medicine.disease, Tissue Donors, eye diseases, Microscopy, Fluorescence, Multiphoton, medicine.anatomical_structure, 030221 ophthalmology & optometry, Collagen, Trabecular meshwork, sense organs, Sclera, Fluorescence anisotropy, Biomedical engineering
Abstract: PURPOSE. To evaluate the potential of third-harmonic generation (THG) microscopy combined with second-harmonic generation (SHG) and two-photon excited fluorescence (2PEF) microscopies for visualizing the microstructure of the human cornea and trabecular meshwork based on their intrinsic nonlinear properties. METHODS. Fresh human corneal buttons and corneoscleral discs from an eye bank were observed under a multiphoton microscope incorporating a titanium-sapphire laser and an optical parametric oscillator for the excitation, and equipped with detection channels in the forward and backward directions. RESULTS. Original contrast mechanisms of THG signals in cornea with physiological relevance were elucidated. THG microscopy with circular incident polarization detected microscopic anisotropy and revealed the stacking and distribution of stromal collagen lamellae. THG imaging with linear incident polarization also revealed cellular and anchoring structures with micrometer resolution. In edematous tissue, a strong THG signal around cells indicated the local presence of water. Additionally, SHG signals reflected the distribution of fibrillar collagen, and 2PEF imaging revealed the elastic component of the trabecular meshwork and the fluorescence of metabolically active cells. CONCLUSIONS. The combined imaging modalities of THG, SHG, and 2PEF provide key information about the physiological state and microstructure of the anterior segment over its entire thickness with remarkable contrast and specificity. This imaging method should prove particularly useful for assessing glaucoma and corneal physiopathologies. (Invest Ophthalmol Vis Sci. 2010;51:2459‐2465) DOI:10.1167/iovs.09-4586
Published: 2010

34. Quantum Yield Measurements of Short-Lived Photoactivation Intermediates in DNA Photolyase: Toward a Detailed Understanding of the Triple Tryptophan Electron Transfer Chain

Author: Andras Lukacs, Marten H. Vos, Martin Byrdin, André P. M. Eker, Klaus Brettel, Viruthachalam Thiagarajan, Molecular Genetics, Photocatalyse et Biohydrogène ( LPB ), Département Biochimie, Biophysique et Biologie Structurale ( B3S ), Institut de Biologie Intégrative de la Cellule ( I2BC ), Université Paris-Sud - Paris 11 ( UP11 ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Université Paris-Sud - Paris 11 ( UP11 ) -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 ), Université Paris-Sud - Paris 11 ( UP11 ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Université Paris-Sud - Paris 11 ( UP11 ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ), CNRS, URA2096, Gif sur Yvette, F-91191, affiliation inconnue, Institut de biologie structurale ( IBS - UMR 5075 ), Université Joseph Fourier - Grenoble 1 ( UJF ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Centre National de la Recherche Scientifique ( CNRS ) -Université Grenoble Alpes ( UGA ), Laboratoire d'optique et biosciences ( LOB ), École polytechnique ( X ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), School of Chemical Sciences and Pharmacy, University of East Anglia, Norwich NR4 7TJ, Department of Cell Biology and Genetics, Medical Genetics Centre, Erasmus University Medical Centre, P.O. Box 2040, 3000 CA Rotterdam, Photocatalyse et Biohydrogène (LPB), Département Biochimie, Biophysique et Biologie Structurale (B3S), 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), Centre National de la Recherche Scientifique (CNRS), Institut de biologie structurale (IBS - UMR 5075 ), Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), 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)-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)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'optique et biosciences (LOB), École polytechnique (X)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Système membranaires, photobiologie, stress et détoxication (SMPSD), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)
Subjects: Photochemistry, [SDV]Life Sciences [q-bio], Flavin group, 010402 general chemistry, 01 natural sciences, Cofactor, Electron Transport, chemistry.chemical_compound, Electron transfer, Escherichia coli, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Physical and Theoretical Chemistry, Photolyase, Flavin adenine dinucleotide, biology, [ SDV ] Life Sciences [q-bio], 010405 organic chemistry, Tryptophan, DNA photolyase, Electron transport chain, 0104 chemical sciences, Kinetics, chemistry, biology.protein, Quantum Theory, Proton-coupled electron transfer, Deoxyribodipyrimidine Photo-Lyase
Abstract: International audience; The light-dependent DNA repair enzyme photolyase contains a unique evolutionary conserved triple tryptophan electron transfer chain (W382−W359−W306 in photolyase from E. coli) that bridges the ∼15 Å distance between the buried flavin adenine dinucleotide (FAD) cofactor and the surface of the protein. Upon excitation of the semireduced flavin (FADH°), electron transfer through the chain leads to formation of fully reduced flavin (FADH−; required for DNA repair) and oxidation of the most remote tryptophan residue W306, followed by its deprotonation. The thus-formed tryptophanyl radical W306°+ is reduced either by an extrinsic reductant or by reverse electron transfer from FADH−. Altogether the kinetics of these charge transfer reactions span 10 orders of magnitude, from a few picoseconds to tens of milliseconds. We investigated electron transfer processes in the picosecond−nanosecond time window bridging the time domains covered by ultrafast pump−probe and "classical" continuous probe techniques. Using a recent dedicated setup, we directly show that virtually no absorption change between 300 ps and 10 ns occurs in wild-type photolyase, implying that no charge recombination takes place in this time window. In contrast, W306F mutant photolyase showed a partial absorption recovery with a time constant of 0.85 ns. In wild-type photolyase, the quantum yield of FADH− W306°+ was found at 19 ± 4%, in reference to the established quantum yield of the long-lived excited state of [Ru(bpy)3]2+. With this yield, the optical spectrum of the excited state of FADH° can be constructed from ultrafast spectroscopic data; this spectrum is dominated by excited state absorption extending from below 450 to 850 nm. The new experimental results, taken together with previous data, allow us to propose a detailed kinetic and energetic scheme of the electron transfer chain. Copyright © 2009 American Chemical Society
Published: 2010

35. Ultrafast dynamics of heme distortion in the O2-sensor of a thermophilic anaerobe bacterium

Author: Michel Negrerie, Julien Sellés, Isabelle Lamarre, Olga N. Petrova, Byung-Kuk Yoo, Pierre Nioche, 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), Laboratoire d'Optique et Biosciences (LOB), École polytechnique (X)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), California Institute of Technology (CALTECH), Biologie du chloroplaste et perception de la lumière chez les micro-algues, Institut de biologie physico-chimique (IBPC (FR_550)), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS), Toxicité environnementale, cibles thérapeutiques, signalisation cellulaire (T3S - UMR_S 1124), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Biomedtech Facilities (UMS 2009 / US36), Gestionnaire, Hal Sorbonne Université, Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), and Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)
Subjects: 0301 basic medicine, inorganic chemicals, Conformational change, Allosteric regulation, Protein domain, 010402 general chemistry, 01 natural sciences, Biochemistry, Dissociation (chemistry), 03 medical and health sciences, chemistry.chemical_compound, [CHIM] Chemical Sciences, Materials Chemistry, Environmental Chemistry, [CHIM]Chemical Sciences, Heme, QD1-999, Histidine, General Chemistry, 0104 chemical sciences, Chemistry, 030104 developmental biology, chemistry, Biophysics, Hemoglobin, Oxygen binding
Abstract: Heme-Nitric oxide and Oxygen binding protein domains (H-NOX) are found in signaling pathways of both prokaryotes and eukaryotes and share sequence homology with soluble guanylate cyclase, the mammalian NO receptor. In bacteria, H-NOX is associated with kinase or methyl accepting chemotaxis domains. In the O2-sensor of the strict anaerobe Caldanaerobacter tengcongensis (Ct H-NOX) the heme appears highly distorted after O2 binding, but the role of heme distortion in allosteric transitions was not yet evidenced. Here, we measure the dynamics of the heme distortion triggered by the dissociation of diatomics from Ct H-NOX using transient electronic absorption spectroscopy in the picosecond to millisecond time range. We obtained a spectroscopic signature of the heme flattening upon O2 dissociation. The heme distortion is immediately (
Published: 2021

36. Characterization of Light-Induced, Short-Lived Interacting Radicals in the Active Site of Flavoprotein Ferredoxin-NADP+ Oxidoreductase

Author: Alexey Aleksandrov, Marten H. Vos, Bo Zhuang, Daisuke Seo, Vos, Marten, Laboratoire d'Optique et Biosciences (LOB), École polytechnique (X)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Division of Material Science, Graduate School of Natural Science and Technology, Kanazawa University, and Kanazawa University (KU)
Subjects: Flavin adenine dinucleotide, chemistry.chemical_classification, biology, Radical, Reactive intermediate, Active site, Flavoprotein, General Chemistry, Reaction intermediate, 010402 general chemistry, Photochemistry, 01 natural sciences, Biochemistry, Catalysis, Cofactor, 0104 chemical sciences, chemistry.chemical_compound, Colloid and Surface Chemistry, chemistry, Oxidoreductase, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, biology.protein, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology
Abstract: International audience; Radicals of flavin adenine dinucleotide (FAD), as well as tyrosine and tryptophan, are widely involved as key reactive intermediates during electron transfer (ET) reactions in flavoproteins. Due to the high reactivity of these species, and their corresponding short lifetime, characterization of these intermediates in functional processes of flavoproteins is usually challenging, but can be achieved by ultrafast spectroscopic studies of light-activatable flavoproteins. In ferredoxin-NADP + oxidoreductase from Bacillus subtilis (BsFNR), fluorescence of the FAD cofactor that very closely interacts with a neighboring tyrosine residue (Tyr50), is strongly quenched. Here we study short-lived photoproducts of this enzyme and its variants with Tyr50 replaced by tryptophan or glycine. Using time-resolved fluorescence and absorption spectroscopies, we show that upon the excitation of WT BsFNR, ultrafast ET from Tyr50 to the excited FAD cofactor occurs in ~260 fs, an order of magnitude faster than the decay by charge recombination, facilitating the characterization of the reaction intermediates in the charge-separated state with respect to other recently studied systems. These studies are corroborated by experiments on the Y50W mutant protein, which yield photoproducts qualitatively similar to those observed in other tryptophan bearing flavoproteins. By combining the experimental results with molecular dynamics simulations and quantum mechanics calculations, we investigate in detail the effect of protein environment and relaxations on the spectral properties of those radical intermediates, and demonstrate that the spectral features of radical anionic FAD are highly sensitive to its environment, and in particular to the dynamics and nature of the counter-ions formed in the photoproducts. Altogether, comprehensive characterizations are provided for important radical intermediates that are generally involved in functional processes of flavoproteins.
Published: 2021

37. Insights into G-Quadruplex–Hemin Dynamics Using Atomistic Simulations: Implications for Reactivity and Folding

Author: Barira Islam, Michal Otyepka, Jielin Chen, David Monchaud, Jiří Šponer, Jean-Louis Mergny, Jun Zhou, Petr Stadlbauer, Institut de Chimie Moléculaire de l'Université de Bourgogne [Dijon] (ICMUB), Centre National de la Recherche Scientifique (CNRS)-Université de Bourgogne (UB)-Institut de Chimie du CNRS (INC), Laboratoire d'Optique et Biosciences (LOB), and École polytechnique (X)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: [SDV.BIO]Life Sciences [q-bio]/Biotechnology, DNAzyme, Guanine, DNA Folding, Deoxyribozyme, Molecular Dynamics Simulation, 010402 general chemistry, G-quadruplex, DNA folding, 01 natural sciences, DNA ligand, 03 medical and health sciences, chemistry.chemical_compound, Molecular dynamics, 0103 physical sciences, Molecule, [INFO]Computer Science [cs], [INFO.INFO-BT]Computer Science [cs]/Biotechnology, Physical and Theoretical Chemistry, 030304 developmental biology, 0303 health sciences, 010304 chemical physics, biology, Molecular dynamics simulations, G-quartet, [CHIM.CATA]Chemical Sciences/Catalysis, DNA, Catalytic, 0104 chemical sciences, Computer Science Applications, G-Quadruplexes, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, Folding (chemistry), chemistry, Quadruplex nucleic acids, Chaperone (protein), Biocatalysis, biology.protein, Biophysics, Hemin, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Biosensor, [CHIM.CHEM]Chemical Sciences/Cheminformatics
Abstract: Guanine quadruplex nucleic acids (G4s) are involved in key biological processes such as replication or transcription. Beyond their biological relevance, G4s find applications as biotechnological tools since they readily bind hemin and enhance its peroxidase activity, creating a G4-DNAzyme. The biocatalytic properties of G4-DNAzymes have been thoroughly studied and used for biosensing purposes. Despite hundreds of applications and massive experimental efforts, the atomistic details of the reaction mechanism remain unclear. To help select between the different hypotheses currently under investigation, we use extended explicit-solvent molecular dynamics (MD) simulations to scrutinize the G4/hemin interaction. We find that besides the dominant conformation in which hemin is stacked atop the external G-quartets, hemin can also transiently bind to the loops and be brought to the external G-quartets through diverse delivery mechanisms. The simulations do not support the catalytic mechanism relying on a wobbling guanine. Similarly, catalytic role of the iron-bound water molecule is not in line with our results, however, given the simulation limitations, this observation should be considered with some caution. The simulations rather suggest tentative mechanisms in which the external G-quartet itself could be responsible for the unique H2O2-promoted biocatalytic properties of the G4/hemin complexes. Once stacked atop a terminal G-quartet, hemin rotates about its vertical axis while readily sampling shifted geometries where the iron transiently contacts oxygen atoms of the adjacent G-quartet. This dynamics is not apparent from the ensemble-averaged structure. We also visualize transient interactions between the stacked hemin and the G4 loops. Finally, we investigated interactions between hemin and on-pathway folding intermediates of the parallel-stranded G4 fold. The simulations suggest that hemin drives the folding of parallel-stranded G4s from slip-stranded intermediates, acting as a G4 chaperone. Limitations of the MD technique are briefly discussed.For Table of Contents Only
Published: 2021

38. Spectroscopic analysis of keratin endogenous signal for skin multiphoton microscopy: erratum

Author: Pena, Ana-Maria, Strupler, Mathias, Boulesteix, Thierry, Godeau, G., Schanne-Klein, Marie-Claire, Laboratoire d'optique et biosciences (LOB), École polytechnique (X)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Paris V University, 1 rue Maurice Arnoux, 91 120 Montrouge, affiliation inconnue, Roura, Denis, Laboratoire d'optique et biosciences ( LOB ), and École polytechnique ( X ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS )
Subjects: [PHYS.PHYS.PHYS-OPTICS] Physics [physics]/Physics [physics]/Optics [physics.optics], [SDV.IB] Life Sciences [q-bio]/Bioengineering, 0303 health sciences, [PHYS.PHYS.PHYS-OPTICS]Physics [physics]/Physics [physics]/Optics [physics.optics], [ PHYS.PHYS.PHYS-OPTICS ] Physics [physics]/Physics [physics]/Optics [physics.optics], 01 natural sciences, Atomic and Molecular Physics, and Optics, 3. Good health, 010309 optics, 03 medical and health sciences, 0103 physical sciences, [SDV.IB]Life Sciences [q-bio]/Bioengineering, [ SDV.IB ] Life Sciences [q-bio]/Bioengineering, 030304 developmental biology
Abstract: International audience; We present corrected versions of the list of authors and of Section 2.1.
Published: 2009

39. Single europium-doped nanoparticles measure temporal pattern of reactive oxygen species production inside cells

Author: Antigoni Alexandrou, Thanh-Liem Nguyen, Pierre-Louis Tharaux, Thierry Gacoin, Didier Casanova, Jean-Pierre Boilot, Latifa Bouzhir-Sima, Cédric Bouzigues, Rivo Ramodiharilafy, Laboratoire d'optique et biosciences ( LOB ), École polytechnique ( X ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de physique de la matière condensée ( LPMC ), École polytechnique ( X ) -Centre National de la Recherche Scientifique ( CNRS ), Paris-Centre de Recherche Cardiovasculaire ( PARCC - U970 ), Hôpital Européen Georges Pompidou [APHP] ( HEGP ) -Université Paris Descartes - Paris 5 ( UPD5 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ), Laboratoire d'optique et biosciences (LOB), École polytechnique (X)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de physique de la matière condensée (LPMC), École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS), Paris-Centre de Recherche Cardiovasculaire (PARCC - UMR-S U970), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Hôpital Européen Georges Pompidou [APHP] (HEGP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO), Université Paris Descartes - Paris 5 (UPD5)-Hôpital Européen Georges Pompidou [APHP] (HEGP), Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Institut National de la Santé et de la Recherche Médicale (INSERM), Hôpital Européen Georges Pompidou [APHP] (HEGP), and Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)
Subjects: Myocytes, Smooth Muscle, Biomedical Engineering, Nanoparticle, chemistry.chemical_element, Molecular Probe Techniques, Bioengineering, Nanotechnology, 02 engineering and technology, Biosensing Techniques, 010402 general chemistry, 01 natural sciences, chemistry.chemical_compound, Mice, Europium, Animals, General Materials Science, Irradiation, Electrical and Electronic Engineering, Particle Size, Hydrogen peroxide, Cells, Cultured, chemistry.chemical_classification, Reactive oxygen species, Hydrogen Peroxide, 021001 nanoscience & nanotechnology, Condensed Matter Physics, Atomic and Molecular Physics, and Optics, 0104 chemical sciences, chemistry, Temporal resolution, Luminescent Measurements, Biophysics, Nanoparticles, 0210 nano-technology, Luminescence, Reactive Oxygen Species, Intracellular
Abstract: Low concentrations of reactive oxygen species, notably hydrogen peroxide (H2O2), mediate various signalling processes in the cell1,2. Production of these signals is highly regulated3 and a suitable probe is needed to measure these events. Here, we show that a probe based on a single nanoparticle can quantitatively measure transient H2O2 generation in living cells. The Y0.6Eu0.4VO4 nanoparticles undergo photoreduction under laser irradiation but re-oxidize in the presence of oxidants, leading to a recovery in luminescence. Our probe can be regenerated and reliably detects intracellular H2O2 with a 30-s temporal resolution and a dynamic range of 1–45 µM. The differences in the timing of intracellular H2O2 production triggered by different signals were also measured using these nanoparticles. Although the probe is not selective towards H2O2, in many signalling processes H2O2 is, however, the dominant oxidant3,4,5,6. In conjunction with appropriate controls, this probe is a powerful tool for unravelling pathways that involve reactive oxygen species. The dynamic production of oxidants inside cells can be quantified by a probe based on a single nanoparticle, offering a tool to monitor and understand how cells regulate their signalling responses.
Published: 2009

40. Multimodal Multiphoton Imaging of Human Eye Tissues

Author: Aptel, Florent, Olivier, Nicolas, Deniset, Ariane, Plamann, Karsten, Denis, P., Legeais, Jean-Marc, Schanne-Klein, Marie-Claire, Beaurepaire, Emmanuel, Service d'Ophtalmologie [Hôpital Edouard Herriot - HCL]], Hôpital Edouard Herriot [CHU - HCL], Hospices Civils de Lyon ( HCL ) -Hospices Civils de Lyon ( HCL ), Laboratoire Biotechnologie et Œil, Université Paris Descartes - Paris 5 ( UPD5 ) -Hôpital Hôtel-Dieu [Paris], Laboratoire d'optique et biosciences ( LOB ), École polytechnique ( X ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire d'optique appliquée ( LOA ), École Nationale Supérieure de Techniques Avancées ( Univ. Paris-Saclay, ENSTA ParisTech ) -École polytechnique ( X ) -Centre National de la Recherche Scientifique ( CNRS ), Le, Thuy, Hospices Civils de Lyon (HCL)-Hospices Civils de Lyon (HCL), Université Paris Descartes - Paris 5 (UPD5)-Hôpital Hôtel-Dieu [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Laboratoire d'optique et biosciences (LOB), École polytechnique (X)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'optique appliquée (LOA), École Nationale Supérieure de Techniques Avancées (ENSTA Paris)-École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS), and Centre National de la Recherche Scientifique (CNRS)-École polytechnique (X)-École Nationale Supérieure de Techniques Avancées (ENSTA Paris)
Subjects: [PHYS.PHYS.PHYS-OPTICS] Physics [physics]/Physics [physics]/Optics [physics.optics], imaging/image analysis: non-clinical, [PHYS.PHYS.PHYS-OPTICS]Physics [physics]/Physics [physics]/Optics [physics.optics], [ PHYS.PHYS.PHYS-OPTICS ] Physics [physics]/Physics [physics]/Optics [physics.optics], genetic structures, sense organs, cornea: basic science, imaging methods (CT FA ICG MRI OCT RTA SLO ultrasound), eye diseases
Abstract: International audience; Purpose:To evaluate three combined modalities of multiphoton microscopy, second-harmonic generation (SHG), third-harmonic generation (THG), and two-photon-excited fluorescence (2PEF) for imaging cornea and trabecular meshwork in human intact eye tissue. Methods:A tunable femtosecond laser chain ( = 700-1250 nm) comprising a titanium-sapphire laser oscillator and an optical parametric oscillator was used to produce 2PEF (380-620nm), SHG (/2=430 or 600nm) and THG (/3= 400nm). Eight corneoscleral discs from eye bank and seven fresh corneal buttons obtained after penetrating keratoplasty were examined with water-immersion objectives. Forward and backward signals were detected and compared. Results:The three imaging modalities provide complementary information on intact tissue over the entire thickness of the cornea. THG imaging reveals the tissue morphology, including the epithelium structure with sub-cellular resolution. Polarization-resolved THG microscopy reveals stromal birefringent domains. In phenol-stained corneas, THG also reveals the keratocytes network. SHG imaging probes the distribution of stromal collagen lamellas organization. 2PEF imaging reveals the elastic component of the extra-cellular matrix and the distribution of fluorescent organelles (i.e. mitochondria) in stromal and epithelial cells. The trabeculum images show the three-dimensional organisation of the trabecular lamellas. Emission is predominantly forward directed for THG and SHG but in some cases, images can be recorded in the epi-direction. Conclusions:The combined imaging modalities of SHG, THG, and 2PEF microscopy are effective methods to evaluate cornea and trabecular meshwork microstructures in situ. This imaging approach should prove particularly appropriate for assessing corneal and glaucoma physiopathology, and might be amenable to in vivo diagnostics.
Published: 2009

41. Red Blood Cell Sickling in Microfluidic droplets

Author: Abbyad, Paul, Baroud, Charles N., Tharaux, Pierre-Louis, Alexandrou, Antigoni, Roura, Denis, Laboratoire d'optique et biosciences ( LOB ), École polytechnique ( X ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire d'hydrodynamique ( LadHyX ), École polytechnique ( X ) -Centre National de la Recherche Scientifique ( CNRS ), Paris-Centre de Recherche Cardiovasculaire ( PARCC - U970 ), Hôpital Européen Georges Pompidou [APHP] ( HEGP ) -Université Paris Descartes - Paris 5 ( UPD5 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ), Laboratoire d'optique et biosciences (LOB), École polytechnique (X)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'hydrodynamique (LadHyX), Centre National de la Recherche Scientifique (CNRS)-École polytechnique (X), Paris-Centre de Recherche Cardiovasculaire (PARCC - UMR-S U970), Université Paris Descartes - Paris 5 (UPD5)-Hôpital Européen Georges Pompidou [APHP] (HEGP), Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Institut National de la Santé et de la Recherche Médicale (INSERM), École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Hôpital Européen Georges Pompidou [APHP] (HEGP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO), Hôpital Européen Georges Pompidou [APHP] (HEGP), and Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)
Published: 2009

42. Photoselection Polarization Experiments Reveal Ultrafast Electron Hopping Between Distinct Aromatic Residues in the Flavoprotein DNA Photolyase

Author: Marten H. Vos, André P. M. Eker, Martin Byrdin, Klaus Brettel, Andras Lukacs, Laboratoire d'optique et biosciences ( LOB ), École polytechnique ( X ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Department of Cell Biology and Genetics, Erasmus University Medical Centre, Service de Bioénergétique, Biologie Stucturale, et Mécanismes ( SB2SM ), Centre National de la Recherche Scientifique ( CNRS ) -Institut de Biologie Intégrative de la Cellule ( I2BC ), Université Paris-Sud - Paris 11 ( UP11 ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Université Paris-Sud - Paris 11 ( UP11 ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ), P. Corkum, S. De Silvestri, K. Nelson, E. Riedle and R.W. Schoenlein, Laboratoire d'optique et biosciences (LOB), École polytechnique (X)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Service de Bioénergétique, Biologie Stucturale, et Mécanismes (SB2SM), 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), P. Corkum, S. De Silvestri, K. Nelson, E. Riedle and R.W. Schoenlein, Institut de Biologie Intégrative de la Cellule (I2BC), 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)-Centre National de la Recherche Scientifique (CNRS)
Subjects: chemistry.chemical_classification, biology, Chemistry, Tryptophan, Flavoprotein, 02 engineering and technology, DNA photolyase, 010402 general chemistry, 021001 nanoscience & nanotechnology, Photochemistry, 01 natural sciences, 0104 chemical sciences, Amino acid, Electron transfer, Directed mutagenesis, Picosecond, biology.protein, 0210 nano-technology, Polarization (electrochemistry)
Abstract: International audience; Flavin-excitation initiated electron transfer along three tryptophan amino acids in DNA photolyase was studied. Combining ultrafast polarization and side directed mutagenesis approaches the chain was shown to allow very efficient long-range transprotein electrontransfer in picoseconds.
Published: 2008

43. L’imagerie optique de nanoparticules luminescentes : de la détection de biomolécules au diagnostic in vitro

Author: Antigoni Alexandrou, Fanny Mousseau, Cedric Bouzigues, Chao Yu, Matière et Systèmes Complexes (MSC (UMR_7057)), Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Laboratoire d'Optique et Biosciences (LOB), and École polytechnique (X)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: [SPI]Engineering Sciences [physics], 3. Good health
Abstract: International audience; Pour détecter des biomolécules et pathogènes (protéines, virus, bactéries, …) avec des sensibilités satisfaisantes, il est actuellement nécessaire d’utiliser des appareils de laboratoires coûteux. En combinant les remarquables propriétés optiques des ions lanthanides à un lecteur simple couplé à un smartphone, nous démontrons comment développer un système de détection portable, rapide et ultrasensible.
Published: 2021

44. Mechanism of Naphthoquinone Selectivity of Thymidylate Synthase ThyX

Author: Alexey Aleksandrov, Hubert F. Becker, Hannu Myllykallio, Myllykallio, Hannu, APPEL À PROJETS GÉNÉRIQUE 2018 - Modèles atomiques précis pour la conception de médicaments assistée par ordinateur - - ATMCADD2018 - ANR-18-CE44-0002 - AAPG2018 - VALID, Laboratoire d'Optique et Biosciences (LOB), École polytechnique (X)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Sorbonne Université (SU), ANR-18-CE44-0002,ATMCADD,Modèles atomiques précis pour la conception de médicaments assistée par ordinateur(2018), and Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École polytechnique (X)
Subjects: Arginine, Stereochemistry, enzyme inhibitors, Biophysics, naphthoquinone, Context (language use), Flavin group, Molecular Dynamics Simulation, Thymidylate synthase, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, binding free energy, 030304 developmental biology, 0303 health sciences, biology, protonation free energy, Rational design, Substrate (chemistry), Uracil, Mycobacterium tuberculosis, Thymidylate Synthase, Articles, flavin, Naphthoquinone, 3. Good health, thymidylate synthase ThyX, chemistry, [SDV.SP.PHARMA] Life Sciences [q-bio]/Pharmaceutical sciences/Pharmacology, [SDV.SP.PHARMA]Life Sciences [q-bio]/Pharmaceutical sciences/Pharmacology, biology.protein, 030217 neurology & neurosurgery, Naphthoquinones
Abstract: International audience; Naphthoquinones (NQs) are natural and synthetic compounds with a wide range of biological activities commonly attributed to their redox activity and/or chemical reactivity. However, genetic and biochemical experiments have recently demonstrated that 2-hydroxy-NQs (2-OH-NQs) act as highly specific non-covalent inhibitors of the essential bacterial thymidylate synthase ThyX in a cellular context. We used biochemical experiments and molecular dynamics simulations to elucidate the selective inhibition mechanism of NQ inhibitors of ThyX from Mycobacterium tuberculosis (Mtb). Free energy simulations rationalized how ThyX recognizes the natural substrate dUMP in the N3 ionized form using an arginine, Arg199 in Mtb. The results further demonstrated that 2-OH-NQ, similarly to dUMP, binds to ThyX in the ionized form and the strong and selective binding of 2-OH-NQ to ThyX is also explained by electrostatic interactions with Arg199. The stronger binding of the close analog 5F-dUMP to ThyX and its inhibitory properties compared to dUMP were explained by the stronger acidity of the uracil N3 atom. Our results, therefore, revealed that the ionization of 2-OH-NQs drives their biological activities by mimicking the interactions with the natural substrate. Our observations encourage the rational design of optimized ThyX inhibitors that ultimately may serve as antibiotics.
Published: 2020

45. Introduction to Femtochemistry: Excited-State Proton Transfer from Pyranine to Water Studied by Femtosecond Transient Absorption

Author: Thomas Gustavsson, Isabelle Lampre, Pascale Changenet, Laboratoire d'Optique et Biosciences (LOB), École polytechnique (X)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Interactions, Dynamiques et Lasers (ex SPAM) (LIDyl), Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Biomolécules Excitées (DICO), 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-Laboratoire Interactions, Dynamiques et Lasers (ex SPAM) (LIDyl), Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut de Chimie Physique (ICP), Institut de Chimie du CNRS (INC)-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), Dynamique et Interactions en phase Condensée (DICO), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), and Changenet, Pascale
Subjects: Photochemistry, Graduate Education/Research, UV−Vis Spectroscopy, 010402 general chemistry, Physical Chemistry, 01 natural sciences, Education, Pyranine, 03 medical and health sciences, chemistry.chemical_compound, [CHIM] Chemical Sciences, Ultrafast laser spectroscopy, Reactions, [CHIM]Chemical Sciences, Stimulated emission, Absorption (electromagnetic radiation), 030304 developmental biology, 0303 health sciences, pH, Lasers, General Chemistry, 0104 chemical sciences, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, Photoexcitation, [CHIM.THEO] Chemical Sciences/Theoretical and/or physical chemistry, Kinetics, chemistry, Femtosecond, Atomic physics, Femtochemistry, Ultrashort pulse
Abstract: International audience; In order to introduce students to the fascinating field of femtochemistry, we propose here a practical laboratory training course conceived for second-year master's students in chemistry. We describe the use of a broadband femtosecond transient absorption (pump−probe) experiment for monitoring a fast light-triggered chemical reaction in solution. The experiments are performed on the pyranine photoacid, which upon photo-excitation at 390 nm undergoes a proton transfer to the solvent in about 90 ps. While this practical course involves advanced equipment and techniques, the measured transient absorption data allow easy analysis and interpretation. The transient absorption spectra at a few selected delay times can be analyzed qualitatively in terms of bleach, induced absorption, and stimulated emission. Likewise, the transient absorption signals at a few chosen wavelengths can be quantitatively analyzed and explained with simple kinetic models to determine the time constant of the proton-transfer reaction. This training aims at giving the students the opportunity to face some of the current challenges in contemporary chemistry by learning the basics of ultrafast spectroscopy.
Published: 2020

46. Allosteric activators modulate the Fe-His bond in soluble guanylate cyclase and in Clostridium botulinum NO-sensor

Author: Négrerie, Michel, Yoo, Byung-Kuk, Lamarre, Isabelle, Rappaport, Fabrice, Nioche, Pierre, Martin, Jean-Louis, Laboratoire d'optique et biosciences (LOB), École polytechnique (X)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie physico-chimique (IBPC), Centre National de la Recherche Scientifique (CNRS), Université Paris Descartes - Faculté des Sciences Fondamentales et Biomédicales (UPD5 Sciences), Université Paris Descartes - Paris 5 (UPD5), Laboratoire d'optique et biosciences ( LOB ), École polytechnique ( X ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Institut de biologie physico-chimique ( IBPC ), Centre National de la Recherche Scientifique ( CNRS ), Université Paris Descartes - Faculté des Sciences Fondamentales et Biomédicales ( UPD5 Sciences ), and Université Paris Descartes - Paris 5 ( UPD5 )
Subjects: ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2006

47. Micrometer scale ex vivo multiphoton imaging of unstained arterial wall structure

Author: Emmanuel Beaurepaire, Thierry Boulesteix, Gaston Godeau, Martin-Pierre Sauviat, Nicole Pages, Marie-Claire Schanne-Klein, Ana-Maria Pena, Laboratoire d'optique et biosciences (LOB), École polytechnique (X)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université Louis Pasteur, Université Louis Pasteur - Strasbourg I, Laboratory of Unmineralized Tissues Physiopathology, Université Paris Descartes - Paris 5 (UPD5), Laboratoire d'optique et biosciences ( LOB ), École polytechnique ( X ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), and Université Paris Descartes - Paris 5 ( UPD5 )
Subjects: Male, collagen, Histology, Materials science, extracellular matrix, elastin, In Vitro Techniques, 01 natural sciences, Pathology and Forensic Medicine, 010309 optics, Micrometre, Extracellular matrix, Rats, Sprague-Dawley, 03 medical and health sciences, medicine.artery, 0103 physical sciences, Microscopy, Image Interpretation, Computer-Assisted, medicine, Animals, 030304 developmental biology, 0303 health sciences, Aorta, biology, two-photon excited fluorescence, artery, tissue, Cell Biology, Anatomy, Coronary Vessels, 3. Good health, Rats, medicine.anatomical_structure, Multiphoton fluorescence microscope, Carotid Arteries, Microscopy, Fluorescence, Multiphoton, multiphoton microscopy, biology.protein, cardiovascular system, Female, Elastin, Ex vivo, Biomedical engineering, Artery, second-harmonic generation
Abstract: Background: We characterize the application of multiphoton microscopy to the observation of the extracellular matrix of fresh unstained vessels. Method: Combined two-photon-excited fluorescence (2PEF) and second harmonic generation (SHG) imaging of large arteries reveals the architecture of elastin and collagen fibers in the vessel wall with remarkable specificity. Results: We present elastin/collagen imaging in unstained rat vessels at both micrometer and whole vessel scales, and we characterize the optical properties of rat carotid artery and aorta walls. We apply this method to evidence deleterious effects of residual doses of a pesticide on the vessel wall. Conclusion: This study illustrates the potential of 2PEF/ SHG microscopy for pharmacological studies in unlabeled arteries. q 2005 International Society for Analytical Cytology
Published: 2006

48. Molecular insights into the role of heme in the transcriptional regulatory system AppA/PpsR

Author: Sofia M. Kapetanaki, Zsuzsanna Fekete, Pierre Dorlet, Marten H. Vos, Ursula Liebl, Andras Lukacs, University of Pécs Medical School (UP MS), University of Pecs, Bioénergétique et Ingénierie des Protéines (BIP ), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Optique et Biosciences (LOB), and École polytechnique (X)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Repressor Proteins, Bacterial Proteins, Flavoproteins, Flavins, Biophysics, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Articles, Gene Expression Regulation, Bacterial, Heme, Rhodobacter sphaeroides, ComputingMilieux_MISCELLANEOUS, Dinucleoside Phosphates
Abstract: International audience; Heme has been shown to have a crucial role in the signal transduction mechanism of the facultative photoheterotrophic bacterium Rhodobacter sphaeroides. It interacts with the transcriptional regulatory complex AppA/PpsR, in which AppA and PpsR function as the antirepressor and repressor, respectively, of photosynthesis gene expression. The mechanism, however, of this interaction remains incompletely understood. In this study, we combined electron paramagnetic resonance (EPR) spectroscopy and Förster resonance energy transfer (FRET) to demonstrate the ligation of heme in PpsR with a proposed cysteine residue. We show that heme binding in AppA affects the fluorescent properties of the dark-adapted state of the protein, suggesting a less constrained flavin environment compared with the absence of heme and the light-adapted state. We performed ultrafast transient absorption measurements in order to reveal potential differences in the dynamic processes in the full-length AppA and its heme-binding domain alone. Comparison of the CO-binding dynamics demonstrates a more open heme pocket in the holo-protein, qualitatively similar to what has been observed in the CO sensor RcoM-2, and suggests a communication path between the blue-light-using flavin (BLUF) and sensing containing heme instead of cobalamin (SCHIC) domains of AppA. We have also examined quantitatively the affinity of PpsR to bind to individual DNA fragments of the puc promoter using fluorescence anisotropy assays. We conclude that oligomerization of PpsR is initially triggered by binding of one of the two DNA fragments and observe a ∼10-fold increase in the dissociation constant Kd for DNA binding upon heme binding to PpsR. Our study provides significant new insight at the molecular level on the regulatory role of heme that modulates the complex transcriptional regulation in R. sphaeroides and supports the two levels of heme signaling, via its binding to AppA and PpsR and via the sensing of gases like oxygen.
Published: 2022

49. Thiosugar naphthalene diimide conjugates: G-quadruplex ligands with antiparasitic and anticancer activity

Author: Efres Belmonte-Reche, Alessandra Benassi, Pablo Peñalver, Anne Cucchiarini, Aurore Guédin, Jean Louis Mergny, Frèdèric Rosu, Valerie Gabelica, Mauro Freccero, Filippo Doria, Juan Carlos Morales, Instituto de Parasitología y Biomedicina 'López Neyra', CSIC, Università degli Studi di Pavia = University of Pavia (UNIPV), Laboratoire d'Optique et Biosciences (LOB), École polytechnique (X)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Imagerie Moléculaire et Nanobiotechnologies - Institut Européen de Chimie et Biologie (IECB), Université Sciences et Technologies - Bordeaux 1 (UB)-Centre National de la Recherche Scientifique (CNRS), Institut Européen de Chimie et Biologie (IECB), Université de Bordeaux (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Acides Nucléiques : Régulations Naturelle et Artificielle (ARNA), Université de Bordeaux (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), and Mergny, Jean-Louis
Subjects: Pharmacology, Antiparasitic, Conjugate, Carbohydrate, Antiparasitic Agents, G-quadruplex, Organic Chemistry, [SDV.BBM.BP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, Ligand, [SDV.CAN]Life Sciences [q-bio]/Cancer, General Medicine, DNA, Naphthalenes, Imides, Ligands, Thiosugars, G-Quadruplexes, [SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, Anticancer, [SDV.CAN] Life Sciences [q-bio]/Cancer, Drug Discovery, Animals, Humans, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, [SDV.MP.PAR] Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology
Abstract: International audience; Glycosyl conjugation to drugs is a strategy being used to take advantage of glucose transporters (GLUT) overexpression in cancer cells in comparison with non-cancerous cells. Its extension to the conjugation of drugs to thiosugars tries to exploit their higher biostability when compared to O-glycosides. Here, we have synthesized a series of thiosugar naphthalene diimide conjugates as G-quadruplex ligands and have explored modifications of the amino sidechain comparing dimethyl amino and morpholino groups. Then, we studied their antiproliferative activity in colon cancer cells, and their antiparasitic activity in T. brucei and L. major parasites, together with their ability to bind quadruplexes and their cellular uptake and location. We observed higher toxicity for the sugar-NDI-NMe2 derivatives than for the sugar-NDI-morph compounds, both in mammalian cells and in parasites. Our experiments indicate that a less efficient binding to quadruplexes and a worse cellular uptake of the carb-NDI-morph derivatives could be the reasons for these differences. We found small variations in cytotoxicity between O-carb-NDIs and S-carb-NDIs, except against non-cancerous human fibroblasts MRC-5, where thiosugar-NDIs tend to be less toxic. This leads to a notable selectivity for β-thiomaltosyl-NDI-NMe212 (9.8 fold), with an IC50 of 0.3 μM against HT-29 cells. Finally, the antiparasitic activity observed for the carb-NDI-NMe2 derivatives against T. brucei was in the nanomolar range with a good selectivity index in the range of 30- to 69- fold.
Published: 2022

50. Screening of Scaffolds for the Design of G-Quadruplex Ligands

Author: Joana Figueiredo, David Peitinho, Maria Paula Cabral Campello, Maria Cristina Oliveira, António Paulo, Jean-Louis Mergny, Carla Cruz, University of Beira Interior [Portugal] (UBI), Universidade de Lisboa = University of Lisbon (ULISBOA), Laboratoire d'Optique et Biosciences (LOB), École polytechnique (X)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institute of Biophysics of the Czech Academy of Sciences (IBP / CAS), Czech Academy of Sciences [Prague] (CAS), and Mergny, Jean-Louis
Subjects: Fluid Flow and Transfer Processes, drug-design, G-quadruplex, Process Chemistry and Technology, scaffolds, General Engineering, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, heterocycle compounds, General Materials Science, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Instrumentation, Computer Science Applications
Abstract: International audience; In the last decade, progress has been made in G-quadruplex (G4) ligands development, but for most compounds, the ligand binding mode is speculative or based on low resolution methods, with its discovery based on structure-based approaches. Herein, we report the synthesis of small (MW < 400 Da) heterocycle compounds, containing different aromatic scaffolds, such as phenyl, quinoline, naphthalene, phenanthroline and acridine moieties, in order to explore their stabilization effect towards different DNA G4s, such as those found in c-MYC, KRAS21 and VEGF promoters, 21G human telomeric motif and pre-MIR150. The fluorescence resonance energy transfer (FRET) melting assay indicates that the acridine moiety is the most active scaffold, followed by phenanthroline. The different scaffolds are promising in terms of drug-like properties and, in general, the IC50 values of the respective heterocycle compounds are lower in a cancer cell line, when compared with a normal cell line. The acridine derivative C5NH2 has the most favorable cytotoxic profile in terms of cell selectivity.
Published: 2022
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