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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.

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

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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).

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.

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.

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

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.

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.

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.

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.

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.

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.

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

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

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 (

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.

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

International audience; We present corrected versions of the list of authors and of Section 2.1.

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.

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.

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.

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.

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

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.

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.

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.

International audience; The photophysical properties of anionic semireduced flavin radicals are largely unknown despite their importance in numerous biochemical reactions. Here, we studied the photoproducts of these intrinsically unstable species in five different flavoprotein oxidases where they can be stabilized, including the well-characterized glucose oxidase. Using ultrafast absorption and fluorescence spectroscopy, we unexpectedly found that photoexcitation systematically results in the oxidation of protein-bound anionic flavin radicals on a time scale of less than ∼100 fs. The thus generated photoproducts decay back in the remarkably narrow 10- to 20-ps time range. Based on molecular dynamics and quantum mechanics computations, positively charged active-site histidine and arginine residues are proposed to be the electron acceptor candidates. Altogether, we established that, in addition to the commonly known and extensively studied photoreduction of oxidized flavins in flavoproteins, the reverse process (i.e., the photooxidation of anionic flavin radicals) can also occur. We propose that this process may constitute an excited-state deactivation pathway for protein-bound anionic flavin radicals in general. This hitherto undocumented photochemical reaction in flavoproteins further extends the family of flavin photocycles.

International audience; In isolated, catalytically inactive, DNA photolyase from Escherichia coli (E. coli), the flavin adenine dinucleotide cofactor is in its neutral radical state FAD?. It can be activated by a unique light-induced reduction of the flavin, a process initiated by the formation of the excited-state FAD?*. As the photophysical properties of this state are essentially unknown, we performed a comparative characterization by femtosecond transient absorption spectroscopy of FAD?* in DNA photolyase from E. coli and glucose oxidase from Aspergillus niger, and of the excited neutral radical flavin mononucleotide (FMN?*) in flavodoxin from Desulfovibrio gigas. In contrast to photolyase, in glucose oxidase and flavodoxin no electron-transfer products are observed after selective excitation of the flavin radical. In glucose oxidase, FAD?* decays to the ground state in 59 ± 5 ps, close to the 80-ps intrinsic lifetime of the excited state in photolyase, and we discuss that the intrinsic lifetime of the excited state of flavin radical in protein environment is in the 50-80 ps range. FMN?* in flavodoxin decays much faster (2.3 ± 0.3 ps), possibly because of quenching by formation of a very short-lived (INF 0.7 ps) electron-transfer intermediate. Spectroscopically, the excited state of FAD? in photolyase displays a pronounced spectral feature that is absent in the other systems studied. Further characterization by polarized photoselection experiments identifies the feature as an additional induced absorption band at ~ 550 nm superimposed on the ground-state bleaching signal. In view of the unique U-shape configuration of FAD in photolyase, we suggest it to reflect a flavin-adenine charge-transfer interaction.

In Escherichia coli photolyase, excitation of the FAD cofactor in its semireduced radical state (FADH • ) induces an electron transfer over ≈15 Å from tryptophan W306 to the flavin. It has been suggested that two additional tryptophans are involved in an electron transfer chain FADH • ← W382 ← W359 ← W306. To test this hypothesis, we have mutated W382 into redox inert phenylalanine. Ultrafast transient absorption studies showed that, in WT photolyase, excited FADH • decayed with a time constant τ ≈ 26 ps to fully reduced flavin and a tryptophan cation radical. In W382F mutant photolyase, the excited flavin was much longer lived (τ ≈ 80 ps), and no significant amount of product was detected. We conclude that, in WT photolyase, excited FADH • is quenched by electron transfer from W382. On a millisecond scale, a product state with extremely low yield (≈0.5% of WT) was detected in W382F mutant photolyase. Its spectral and kinetic features were similar to the fully reduced flavin/neutral tryptophan radical state in WT photolyase. We suggest that, in W382F mutant photolyase, excited FADH • is reduced by W359 at a rate that competes only poorly with the intrinsic decay of excited FADH • (τ ≈ 80 ps), explaining the low product yield. Subsequently, the W359 cation radical is reduced by W306. The rate constants of electron transfer from W382 to excited FADH • in WT and from W359 to excited FADH • in W382F mutant photolyase were estimated and related to the donor–acceptor distances.

To extend the frontier of genome editing and enable editing of repetitive elements of mammalian genomes, we made use of a set of dead-Cas9 base editor (dBE) variants that allow editing at tens of thousands of loci per cell by overcoming the cell death associated with DNA double-strand breaks and single-strand breaks. We used a set of gRNAs targeting repetitive elements—ranging in target copy number from about 32 to 161 000 per cell. dBEs enabled survival after large-scale base editing, allowing targeted mutations at up to ∼13 200 and ∼12 200 loci in 293T and human induced pluripotent stem cells (hiPSCs), respectively, three orders of magnitude greater than previously recorded. These dBEs can overcome current on-target mutation and toxicity barriers that prevent cell survival after large-scale genome engineering.

Temporin-SHa (SHa) is a small cationic host defence peptide (HDP) produced in skin secretions of the Sahara frog Pelophylax saharicus. This peptide has a broad-spectrum activity, efficiently targeting bacteria, parasites and viruses. Noticeably, SHa has demonstrated an ability to kill Leishmania infantum parasites (amastigotes) within macrophages. Recently, an analog of SHa with an increased net positive charge, named [K3]SHa, has been designed to improve those activities. SHa and [K3]SHa were both shown to exhibit leishmanicidal activity mainly by permeabilization of cell membranes but could also induce apoptotis-like death. Temporins are usually poorly active against Gram-negative bacteria whereas many of these species are of public health interest. Among them, Legionella pneumophila, the etiological agent of Legionnaire’s disease, is of major concern. Indeed, this bacterium adopts an intracellular lifestyle and replicate inside alveolar macrophages likewise inside its numerous protozoan hosts. Despite several authors have studied the antimicrobial activity of many compounds on L. pneumophila released from host cells, nothing is known about activity on intracellular L. pneumophila within their hosts, and subsequently mechanisms of action that could be involved. Here, we showed for the first time that SHa and [K3]SHa were active towards several species of Legionella. Both peptides displayed bactericidal activity and caused a loss of the bacterial envelope integrity leading to a rapid drop in cell viability. Regarding amoebae and THP-1-derived macrophages, SHa was less toxic than [K3]SHa and exhibited low half maximal lethal concentrations (LC50). When used at non-toxic concentration (6.25 µM), SHa killed more than 90% L. pneumophila within amoebae and around 50% within macrophages. Using SHa labeled with the fluorescent dye Cy5, we showed an evenly diffusion within cells except in vacuoles. Moreover, SHa was able to enter the nucleus of amoebae and accumulate in the nucleolus. This subcellular localization seemed specific as macrophages nucleoli remained unlabeled. Finally, no modifications in the expression of cytokines and HDPs were recorded when macrophages were treated with 6.25 µM SHa. By combining all data, we showed that temporin-SHa decreases the intracellular L. pneumophila load within amoebae and macrophages without being toxic for eukaryotic cells. This peptide was also able to reach the nucleolus of amoebae but was not capable to penetrate inside vacuoles. These data are in favor of an indirect action of SHa towards intracellular Legionella and make this peptide a promising template for further developments.

Blue Light Using Flavin (BLUF) domains are increasingly being adopted for use in optogenetic constructs. Despite this, much remains to be resolved on the mechanism of their activation. The advent of unnatural amino acid mutagenesis opens up a new toolbox for the study of protein structural dynamics. The tryptophan analogue, 7-aza-Trp (7AW) was incorporated in the BLUF domain of the Activation of Photopigment and pucA (AppA) photoreceptor in order to investigate the functional dynamics of the crucial W104 residue during photoactivation of the protein. The 7-aza modification to Trp makes selective excitation possible using 310 nm excitation and 380 nm emission, separating the signals of interest from other Trp and Tyr residues. We used Förster energy transfer (FRET) between 7AW and the flavin to estimate the distance between Trp and flavin in both the light- and dark-adapted states in solution. Nanosecond fluorescence anisotropy decay and picosecond fluorescence lifetime measurements for the flavin revealed a rather dynamic picture for the tryptophan residue. In the dark-adapted state, the major population of W104 is pointing away from the flavin and can move freely, in contrast to previous results reported in the literature. Upon blue-light excitation, the dominant tryptophan population is reorganized, moves closer to the flavin occupying a rigidly bound state participating in the hydrogen-bond network around the flavin molecule.

International audience; Rebuilding biological environments is crucial when facing the challenges of fundamental and biomedical research. Thus, preserving the native state of biomolecules is essential. We use electrospinning (ES), which is an extremely promising method for the preparation of fibrillar membranes to mimic the ECM of native tissues. Here, we report for the first time (1) the ES of pure and native collagen into a self-supported membrane in absence of crosslinker and polymer support, (2) the preservation of the membrane integrity in hydrated media in absence of crosslinker and (3) the preservation of the native molecular structure and recovery of the hierarchical assembly of collagen. We use a multiscale approach to characterize collagen native structure at the molecular level using circular dichroism, and to investigate collagen hierarchical organization within the self-supported membrane using a combination of multiphoton and electron microscopies. Finally, we show that the membranes are perfectly suited for cell adhesion and spreading, making them very promising candidates for the development of biomaterials and finding applications in biomedical research.

G-quadruplexes (G4s) are four-stranded nucleic acid structures formed by the stacking of G-tetrads. Here we investigated their formation and function during HIV-1 infection. Using bioinformatics and biophysics analyses we first searched for evolutionary conserved G4-forming sequences in HIV-1 genome. We identified 10 G4s with conservation rates higher than those of HIV-1 regulatory sequences such as RRE and TAR. We then used porphyrin-based G4-binders to probe the formation of the G4s during infection of human cells by native HIV-1. The G4-binders efficiently inhibited HIV-1 infectivity, which is attributed to the formation of G4 structures during HIV-1 replication. Using a qRT-PCR approach, we showed that the formation of viral G4s occurs during the first 2 h post-infection and their stabilization by the G4-binders prevents initiation of reverse transcription. We also used a G4-RNA pull-down approach, based on a G4-specific biotinylated probe, to allow the direct detection and identification of viral G4-RNA in infected cells. Most of the detected G4-RNAs contain crucial regulatory elements such as the PPT and cPPT sequences as well as the U3 region. Hence, these G4s would function in the early stages of infection when the viral RNA genome is being processed for the reverse transcription step.

In the first part of the thesis, we revealed the distribution of EGF receptors and CD9 in the membrane of parietal epithelial cells (PEC) that are involved in inflammatory kidney diseases. First, we used the dSTORM technique to quantitatively map the localization of these proteins in the cell membrane and demonstrate their colocalization in parietal epithelial cells. These proteins are found to be localized in small domains with a radius of about 50 nm - 100 nm in the membrane of PEC cells. In the second part, we used a technique complementary to dSTORM, the single-particle tracking technique,to study the dynamics of the proteins in the cell membrane of different cell types. To analyze the trajectory obtained from singleparticle tracking, we introduced a new method to determine the free and confined portions of the protein motions. The confinement of EGFR was also analyzed by Bayesian inference to extract the confinement characteristics, the stiffness of the harmonic confining potential and the diffusion coefficient. We showed that the confinement characteristics depend on the cell type., Dans la première partie de la thèse, nous avons révélé la distribution des récepteurs à l’EGF (EGFR) et du CD9 dans la membrane des cellules épithéliales pariétales (PEC) impliquées dans des maladies rénales inflammatoires. Dans un premier temps, nous avons utilisé la technique dSTORM pour cartographier quantitativement la localisation de ces protéines dans la membrane cellulaire et démontrer leur colocalisation dans les cellules épithéliales pariétales. Ces protéines sont localisées dans de petits domaines d’un rayon d’environ 50 nm à 100 nm dans la membrane des cellules PEC.Dans la deuxième partie, nous avons utilisé une technique complémentaire à dSTORM, latechnique de suivi de particules uniques pour étudier la dynamique des récepteurs à l’EGF dans la membrane de différents types cellulaires. Pour analyser la trajectoire de suivi d’une seule particule, nous avons introduit une nouvelle méthode pour déterminer les parties libres et confinées des mouvements des protéines. Le confinement des récepteurs EGFR a ensuite été analysé par inférence Bayésienne pour extraire les caractéristiques de confinement, la raideur du potentiel de confinement harmonique et le coefficient de diffusion. Nous avons montré que ces caractéristiques varient d’un type cellulaire à l’autre.

International audience; Three-photon excitation has recently been demonstrated as an effective method to perform intravital microscopy in deep, previously inaccessible regions of the mouse brain. The applicability of 3-photon excitation for deep imaging of other, more heterogeneous tissue types has been much less explored. In this work, we analyze the benefit of high-pulse-energy 1 MHz pulse-repetition-rate infrared excitation near 1300 and 1700 nm for in-depth imaging of tumorous and bone tissue. We show that this excitation regime provides a more than 2-fold increased imaging depth in tumor and bone tissue compared to the illumination conditions commonly used in 2-photon excitation, due to improved excitation confinement and reduced scattering. We also show that simultaneous 3- and 4-photon processes can be effectively induced with a single laser line, enabling the combined detection of blue to far-red fluorescence together with second and third harmonic generation without chromatic aberration, at excitation intensities compatible with live tissue imaging. Finally, we analyze photoperturbation thresholds in this excitation regime and derive setpoints for safe cell imaging. Together, these results indicate that infrared high-pulse-energy low-repetition-rate excitation opens novel perspectives for intravital deep-tissue microscopy of multiple parameters in strongly scattering tissues and organs.

The Caenorhabditis elegans model has greatly contributed to the understanding of the role of G-quadruplexes in genomic instability. The GGCTTA repeats of the C. elegans telomeres resemble the GGGTTA repeats of the human telomeres. However, the comparison of telomeric sequences (Homo sapiens, Tetrahymena, Oxytricha, Bombyx mori and Giardia) revealed that small changes in these repeats can drastically change the topology of the folded G-quadruplex. In the present work we determined the structure adopted by the C. elegans telomeric sequence d[GG(CTTAGG)3]. The investigated C. elegans telomeric sequence is shown to fold into an intramolecular two G-tetrads basket type G-quadruplex structure that includes a C–T base pair in the diagonal loop. This work sheds light on the telomeric structure of the widely used C. elegans animal model.