Publications

2023

• Non-invasive quantitative characterization of varnish thickness on gilt leather by line-field confocal optical coherence tomography
  
  • Galante Giulia
  • Vilbert Maëlle
  • Robinet Laurianne
  • Schanne-Klein Marie-Claire
  • Latour Gaël
  Proceedings of SPIE, the International Society for Optical Engineering, SPIE, The International Society for Optical Engineering, 2023, 12620, pp.1262006. Line-field confocal optical coherence tomography (LC-OCT) is an alternative to conventional OCT that combines OCT and confocal microscopy. This technique gives access to three-dimensional (3D) images with a micrometer resolution in the three spatial directions and enhances signal from the deepest layers within the material. After an experimental determination of the device characteristics, the technique is used for the investigation of16 th to 18 th century fragments of gilt leathers wall-hangings. In these objects, the various layers within the varnish can be identified and the effect of a restoration treatment can be observed to validate the varnish removal process. (10.1117/12.2672564)
  DOI : 10.1117/12.2672564
• The paradoxes of Mycobacterium tuberculosis molecular evolution and consequences for the inference of tuberculosis emergence date
  
  • Zein Eddine Rima
  • Hak F.
  • Le Meur A.
  • Genestet C.
  • Dumitrescu O.
  • Guyeux C.
  • Senelle G.
  • Sola C.
  • Refrégier G.
  Tuberculosis, Elsevier, 2023, 143, pp.102378. The date of Mycobacterium tuberculosis complex emergence has been the subject of long debates. New studies joining archaeological efforts with sequencing methods raise high hopes for solving whether this emergence is closer to 70,000 or to 6000 years before present. Inferring the date of emergence of this pathogen based on sequence data requires a molecular clock. Several clocks inferred from different types of loci and/or different samples, using both sound reasoning and reliable data, are actually very different, which we refer to as the paradoxes of M. tuberculosis molecular evolution. After having presented these paradoxes, we will remind the limits of the molecular clocks used in the different studies such as the assumption of homogeneous substitution rate. We will then review recent results that shed new light on the characteristics of M. tuberculosis molecular evolution: traces of diverse selection pressures, the impact of host dynamics, etc. We provide some ideas on what to do next to get nearer to a reliable dating of Mycobacterium tuberculosis complex emergence. Among them, the collection of additional remains from ancient tuberculosis seems still essential. (10.1016/j.tube.2023.102378)
  DOI : 10.1016/j.tube.2023.102378
• Quadruplexes and aging: G4-binding proteins regulate the presence of miRNA in small extracellular vesicles (sEVs)
  
  • Brázda Václav
  • Mergny Jean-Louis
  Biochimie, Elsevier, 2023, pp.S0300-9084(23)00014-7. The interaction between proteins and nucleic acids is a core element of life. Many proteins bind nucleic acids via a sequence-specific manner, but there are also many types of proteins that recognize various structural motifs. Researchers have recently found that proteins that can recognize DNA and RNA G- quadruplexes (G4s) are very important for basic cellular processes, particularly in eukaryotes. Some of these proteins are located outside the nucleus and interact with RNA, potentially affecting miRNA functions in intercellular communication, which is facilitated by small extracellular vesicles (sEVs). Im- balances in the production of sEVs are associated with various pathologies and senescence in humans. The distribution of miRNA into sEVs is regulated by two RNA-binding proteins, Alyref and FUS. Both proteins possess G-rich recognition motifs that are compatible with the formation of RNA parallel G4 structures. This lends credence to the new hypothesis that G4-formation in RNAs and their interaction with G4-binding proteins can affect the fate of miRNAs and control their distribution in sEVs that are associated with senescence and aging. (10.1016/j.biochi.2023.01.014)
  DOI : 10.1016/j.biochi.2023.01.014
• A sodium / potassium switch for G4-prone G / C-rich sequences
  
  • Luo Yu
  • Živković Martina Lenarčič
  • Wang Jiawei
  • Ryneš Jan
  • Foldynová-Trantírková Silvie
  • Trantírek Lukáš
  • Verga Daniela
  • Mergny Jean-Louis
  Nucleic Acids Research, Oxford University Press, 2023, 52 (1), pp.448-461. Metal ions are essential components for the survival of living organisms. For most species, intracellular and extracellular ionic conditions differ significantly. As G-quadruple x es (G4s) are ion-dependent structures, changes in the [Na+]/[K+] ratio may affect the folding of genomic G4s. More than 11000 putative G4 sequences in the human genome (hg19) contain at least two runs of three continuous cytosines, and these mixed G/C-rich sequences may form a quadruplex or a competing hairpin structure based on G-C base pairing. In this study, we examine how the [Na+]/[K+] ratio influences the structures of G/C-rich sequences. The natural G4 structure with a 9-nt long central loop, CEBwt, was chosen as a model sequence, and the loop bases were gradually replaced by cytosines. The series of CEB mutations revealed that the presence of cytosines in G4 loops does not prevent G4 f olding or decrease G4 stability but increases the probability of forming a competing structure, either a hairpin or an intermolecular duplex. Slow conversion to the quadruplex in vitro (in a potassium-rich buffer) and cells was demonstrated by NMR. 'Shape-shifting' sequences may respond to [Na+]/[K+] changes with delayed kinetics. (10.1093/nar/gkad1073)
  DOI : 10.1093/nar/gkad1073
• Terahertz Spectroscopy Sheds Light on Real‐Time Exchange Kinetics Occurring through Plasma Membrane during Photodynamic Therapy Treatment
  
  • Zheng Xiujun
  • Lordon Blandine
  • Mingotaud Anne‐françoise
  • Vicendo Patricia
  • Brival Rachel
  • Fourquaux Isabelle
  • Gibot Laure
  • Gallot Guilhem
  Advanced Science, Wiley Open Access, 2023, 10 (18), pp.e2300589. 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. (10.1002/advs.202300589)
  DOI : 10.1002/advs.202300589
• Label-free single-cell live imaging reveals fast metabolic switch in T lymphocytes
  
  • Paillon Noémie
  • Ung Thi Phuong Lien
  • Dogniaux Stéphanie
  • Stringari Chiara
  • Hivroz Claire
  Molecular Biology of the Cell, American Society for Cell Biology, 2023. T cell activation induces a metabolic switch generating energy for proliferation, survival, and functions. We used non-invasive label-free two-photon fluorescence lifetime microscopy (2P-FLIM) to map the spatial and temporal dynamics of the metabolic NAD(P)H co-enzyme during T lymphocyte activation. This provides a readout of the OXPHOS and glycolysis rates at a single cell level. Analyzes were performed in the CD4+ leukemic T cell line Jurkat, and in human CD4+ primary T cells. Cells were activated on glass surfaces coated with activating antibodies mimicking immune synapse formation. Comparing the fraction of bound NAD(P)H between resting and activated T cells, we show that T cell activation induces a rapid switch toward glycolysis. This occurs after 10 minutes and remains stable for one hour. Three-dimensional analyzes revealed that the intracellular distribution of fraction of bound NAD(P)H increases at the immune synapse in activated cells. Finally, we show that fraction of bound NAD(P)H tends to negatively correlate with spreading of activated T cells, suggesting a link between actin remodeling and metabolic changes. This study highlights that 2P-FLIM measurement of fraction of bound NAD(P)H is well suited to follow a fast metabolic switch in 3D, in single T lymphocytes with subcellular resolution. (10.1091/mbc.E23-01-0009)
  DOI : 10.1091/mbc.E23-01-0009
• Simple Postsynthesis Thermal Treatment toward High Luminescence Performance of Rare Earth Vanadate Nanoparticles
  
  • Perrella Rafael Vieira
  • Mohammedi Rabei
  • Kuhner Robin
  • Cardone Christophe
  • Larquet Eric
  • Alexandrou Antigoni
  • de Sousa Filho Paulo Cesar
  • Gacoin Thierry
  Crystal Growth & Design, American Chemical Society, 2023, 23 (8), pp.5389-5396. Optical applications of colloidal oxide nanoparticles are often limited by low luminescence efficiencies caused by poor crystallinity and surface quenching. Bulk oxides prepared via conventional high-temperature annealing offer intense luminescence but commonly fail to yield stable colloidal dispersions. Coupling the best of these two situations to afford highly crystalline, dispersible nanoparticles with luminescence performance exceeding bulk solids is still challenging, thus requiring new safe, scalable, and reproducible methodologies. Herein we report a silicate-coating strategy followed by aggregate elimination to recover stable colloids of 40-150 nm single crystalline rare earth vanadates after unprotected annealing (800-1000 °C). Eu3+-doped nanoparticles showed enhanced photostability and ~50% emission quantum yields in water (λexc=280 nm), while Dy3+-, Tm3+-, and Yb3+/Er3+-doped vanadates provided remarkably intense multicolour emissions via downshift or upconversion luminescence. We correlated spectroscopic properties of pristine and annealed solids to microstructural characteristics to explain the superior emission features, opening new perspectives for sensing applications. (10.1021/acs.cgd.3c00308)
  DOI : 10.1021/acs.cgd.3c00308