Publications

2023

• 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
• 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
• 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
• 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
• Evaluation of Slowfade Diamond as a buffer for STORM microscopy
  
  • Boukhatem Hadjer
  • Durel Beatrice
  • Raimbault Manon
  • Laurent Audrey
  • Olivier Nicolas
  Biomedical optics express, Optical Society of America - OSA Publishing, 2023, 14 (2), pp.550. 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. (10.1364/BOE.473463)
  DOI : 10.1364/BOE.473463
• Collective cell migration due to guidance-by-followers is robust to multiple stimuli
  
  • Müller Robert
  • Boutillon Arthur
  • Jahn Diego
  • Starruß Jörn
  • David Nicolas B
  • Brusch Lutz
  Frontiers in Applied Mathematics and Statistics, Frontiers Media S.A, 2023, 9, pp.1163583. Collective cell migration is an important process during biological development and tissue repair but may turn malignant during tumor invasion. Mathematical and computational models are essential to unravel the mechanisms of self-organization that underlie the emergence of collective migration from the interactions among individual cells. Recently, guidance-by-followers was identified as one such underlying mechanism of collective cell migration in the embryo of the zebrafish. This poses the question of how the guidance stimuli are integrated when multiple cells interact simultaneously. In this study, we extend a recent individual-based model by an integration step of the vectorial guidance stimuli and compare model predictions obtained for different variants of the mechanism (arithmetic mean of stimuli, dominance of stimulus with largest transmission interface, and dominance of most head-on stimulus). Simulations are carried out and quantified within the modeling and simulation framework Morpheus. Collective cell migration is found to be robust and qualitatively identical for all considered variants of stimulus integration. Moreover, this study highlights the role of individual-based modeling approaches for understanding collective phenomena at the population scale that emerge from cell-cell interactions. (10.3389/fams.2023.1163583)
  DOI : 10.3389/fams.2023.1163583