Publications

2025

• Role of Neural Crest Cells in Establishing Corneal Transparency During Embryonic Development in Mice
  
  • Ghoubay Djida
  • Vidal Cecile
  • Rappeneau Quentin
  • Emini Jasmina
  • Gitton Yorick
  • Fouquet Stephane
  • Schanne-Klein Marie-Claire
  • Plamann Karsten
  • Latour Gael
  • Borderie Vincent
  , 2025. This study deciphers the exquisitely timed cellular and molecular symphony orchestrating corneal development in mice, revealing how neural crest cells-NCCs transition from multipotent progenitors to architects of a light-transmitting, mechanically robust stroma. Between embryonic day 10 until birth, NCCs undergo posteroanterior differentiation marked by sequential downregulation of stemness markers, paralleled by collagen I deposition initiating at E12. Stromal expansion and keratocyte-driven ECM remodelling yield precisely aligned collagen fibrils within lamellae a configuration enabling transparency through destructive interference of scattered light. Keratocytes adopt a dendritic morphology to minimize light scatter, while secreting crystallin-like proteins that match refractive indices between cells and matrix. Corneal endothelial maturation and dynamic ECM stratification culminate in a tissue optimized for both optical clarity and structural resilience. Our study elucidates the complex choreography of cellular and molecular events underpinning corneal development, offering novel insights into the acquisition of the cornea's unique optical and biomechanical properties. (10.64898/2025.12.08.692921)
  DOI : 10.64898/2025.12.08.692921
• Deciphering the intermolecular interactions between G-quadruplex (G4)-forming sequences
  
  • Xia Jianjun
  • Zhou Jiahang
  • Zhuang Xinzhe
  • Ju Huangxian
  • Monchaud David
  • Chaires Jonathan B
  • Šponer Jiří
  • Mergny Jean-Louis
  • Zhou Jun
  Nucleic Acids Research, Oxford University Press, 2025, 53 (22). <div><p>Interactions between biomolecules govern cellular biology. While protein/protein and protein/nucleic acid (DNA, RNA) interactions-and, to a lesser extent, RNA/RNA and RNA/DNA interactions-ha v e been e xtensiv ely described, a question remains as to whether and how non-canonical DNA str uct ures might interact with each other. This is of particular interest for guanine (G)-rich sequences that can fold into G-quadruplex (G4) str uct ures: Individual G4s are currently studied for their involvement in a myriad of cellular events (mostly pertaining to the control of gene expression), and, more recently, the interactions between two G4s have been scrutinized as being part of a novel gene expression regulatory mechanism in v olving chromatin remodeling through G4-mediated loop f ormation. T he question that needs to be answered is whether G4s or their corresponding G-rich sequences are in v olv ed. We present here a series of results collected using a combination of sequences, experimental conditions, and tec hniques, whic h led us to the conclusion that G4/G4 intermolecular interactions are mostly go v erned b y primary sequence interactions in vitro.</p></div> (10.1093/nar/gkaf1288)
  DOI : 10.1093/nar/gkaf1288
• Label-free nonlinear microscopy probes cellular metabolism and myelin dynamics in live tissue
  
  • Asadipour Bahar
  • Morizet Josephine
  • Ronzano Remi
  • Zhang Xingjian
  • Aigrot Marie-Stephane
  • Mahou Pierre
  • Solinas Xavier
  • Phan Minh Son
  • Chessel Anatole
  • Stankoff Bruno
  • Desmazieres Anne
  • Beaurepaire Emmanuel
  • Stringari Chiara
  Communications Biology, Nature Publishing Group, 2025. Metabolic coupling between neurons and glial cells plays a critical role in brain activity and myelin plasticity. Understanding its role in physiological and pathological contexts requires advanced methods to map metabolism and myelin in live tissue with high spatiotemporal resolution. Here, we present a label-free, multimodal, nonlinear optical microscopy platform integrated with an advanced image processing framework that simultaneously maps cellular metabolism and myelin distribution in organotypic cerebellar cultures. We combine third-harmonic generation microscopy for high-resolution myelin imaging with single axon precision with two-photon fluorescence lifetime microscopy of NAD(P)H metabolic biomarker to assess redox states with single-cell resolution. We introduce automated image analysis methods for cell segmentation and myelinated axon detection, enabling quantitative metabolic and myelin assessment in intact tissue during experimental myelination, demyelination and remyelination. Using this framework, we map the 3D myelin distribution in cerebellar folia and identify distinct metabolic signatures in neurons, oligodendrocytes, and microglia. Furthermore, we measure a metabolic shift in microglia along with myelin distribution changes during experimental demyelination. In conclusion, we establish label-free optical imaging as a powerful tool for the non-invasive characterization of neuro-glial metabolic coupling and myelin organization in living brain tissue, opening new perspectives for research in neuroinflammation and neurodegeneration. (10.1038/s42003-025-09192-4)
  DOI : 10.1038/s42003-025-09192-4
• Study on and off axis of levitation induced by a rotating permanent magnet
  
  • Schreckenberg Hugo
  • El Omari El Alaoui Zayneb
  • Gallot Guilhem
  , 2025. A slightly tilted permanent magnet rotating at high speed can induce a magnetic field capable of trapping another permanent magnet in a non-gravitational dependent levitated bound state, bypassing Earnshaw's theorem. During levitation, the floater magnet is locked in a conical orbit at the same frequency as the rotor. This rotation allows the sides of the same polarity of each magnet to face each other, which is responsible for the dynamic equilibrium of the floater magnet. Here, we theoretically explain the motion of the floater in-axis and off-axis and highlight levitation stability conditions and their dependence on the size of the floater and the speed of the rotor. We experimentally studied the levitation conditions with respect to the angular velocity of the rotor for different floater's sizes and shapes. We observed and analyzed the lower and upper limits of levitation. Finally, we explained the off-axis motion of the center of mass of the floater from its equilibrium position by an extension of the dipole moment model.
• Consensus guidelines for cellular label-free optical metabolic imaging: ensuring accuracy and reproducibility in metabolic profiling
  
  • Georgakoudi Irene
  • Skala Melissa
  • Quinn Kyle
  • Stringari Chiara
  • Sorrells Janet
  • Heikal Ahmed
  • Li Lin
  • Xu He
  • You Sixian
  • Walsh Alex
  • Datta Rupsa
  • Samimi Kayvan
  • Gillette Amani
  • Eliceiri Kevin
  • Balu Mihaela
  • Boppart Stephen
  • Digman Michelle
  • Dunning Kylie
  • Evans Conor
  • Garcia Alba Alfonso
  • Houston Jessica
  • Hwang Wonsang
  • Lindley Matthew
  • Li Xingde
  • Liu Zhiyi
  • Marcu Laura
  • Murugkar Sangeeta
  • Nichols Michael
  • Niesner Raluca
  • Parekh Sapun
  • Rajaram Narasimhan
  • Ranjit Suman
  • Shen Keyue
  • Shi Lingyan
  • Torrado Belén
  • Vallmitjana Alexander
  • Wang-Evers Michael
  • Zemp Roger
  Journal of Biomedical Optics, Society of Photo-optical Instrumentation Engineers, 2025, 30 (S2), pp.S23901. Significance: Cellular metabolism plays a central role in health and disease, making its study critical for advancing diagnostics and therapies. Label-free optical metabolic imaging using endogenous fluorescence from reduced nicotinamide adenine dinucleotide (phosphate) [NAD(P)H] and flavin adenine dinucleotide (FAD) provides nondestructive, high-resolution insights into metabolic function and heterogeneity from the sub-cellular to the tissue level. Standardized approaches are essential to ensure reproducibility and comparability across studies. Aim: We aim to establish a consensus framework for the acquisition, calibration, and reporting of microscopic imaging metabolic function assessments based on fluorescence intensity and lifetime measurements of NAD(P)H and FAD. Approach: We present best practices for calibrating, analyzing, and reporting fluorescence intensity-based optical redox ratios and fluorescence lifetime data using multiexponential fitting and phasor analysis. Guidelines for validation experiments and cross-system standardization are provided to improve accuracy and reproducibility. Results: We demonstrate the importance of calibration procedures and normalization strategies for intensity-based optical redox measurements. We highlight needed calibration, signal-to-noise ratio considerations, and the impact of distinct analytical approaches on fluorescence lifetime-based metabolic function metrics. Conclusion: We recommend a consistent, practical framework for reproducible, label-free, optical metabolic imaging, facilitating robust comparisons across studies and supporting the broader adoption of optical metabolic imaging technologies for biomedical research and clinical translation. (10.1117/1.JBO.30.S2.S23901)
  DOI : 10.1117/1.JBO.30.S2.S23901
• Étude de la dynamique de réplication de l'archée polyploïde Haloferax volcanii à l'échelle nanométrique
  
  • Noury Dorian
  , 2025. La réplication de l'ADN est un processus essentiel pour la prolifération de tous les êtres vivants, en assurant le maintien de l'information génétique à la descendance cellulaire. Le mécanisme de réplication est largement conservé dans les trois domaines du vivant, bien que la composition du réplisome diffère grandement entre bactéries et eucaryotes. Les archées ont un réplisome qui se rapproche de celui de la machinerie eucaryote, faisant d'elles des organismes particulièrement intéressant pour l'étude de la réplication.Nous nous sommes ainsi intéressé à la réplication de l'ADN chez Haloferax volcanii, espèce modèle des Haloarchaeota. H. volcanii est un organisme au profil particulier concernant la réplication : un chromosome circulaire, mais avec 4 origines de réplication, et un nombre de copies élevé et hétérogène. Pour étudier la réplication dans une population aussi complexe, l'équipe a pu observer la protéine de réplication essentielle Rpa2, qui se lie à l'ADN simple brin au niveau du brin retardé. Cette première étude a montré que la protéine localisait sous la forme de foyers, dont la distribution large semble être le reflet de l'hétérogénéité de la population. Face au faible nombre de foyers détectés en comparaison du nombre de fourches potentielle, le passage à des méthodes de super-résolution est nécessaire pour comprendre plus finement la résolution.J'ai donc implémenté l'imagerie en directSTORM de la protéine Rpa2 dans les cellules h. volcanii fixées, ainsi qu'un dispositif d'analyse d'image robuste pour la détection des foyers, permettant de tirer pleinement parti du plus haut niveau d'informations disponibles. Nos résultats suggèrent qu'en prolifération exponentielle H. volcanii réplique son ADN en permanence. La dynamique de réplication observée apparaît étroitement liée à la taille des cellules et à leur quantité d'ADN, de manière quasiment linéaire : les cellules les plus grandes sont aussi celles qui ont le plus d'ADN et le plus grand nombre de foyers de réplication. Ce profil original nous a conduits à supposer une régulation de la réplication de la réplication qui s'apparente à une probabilité uniforme d'initiation par origine de réplication.J'ai pu étendre cette étude à la localisation de Rpa2 dans un mutant délété des quatre origines de réplication. Le mutant présente une organisation très similaire à celle de la souche sauvage dans des conditions optimales, mais moins conservée à plus basse température. Ces premiers résultats soulignent la complexité de la régulation de la réplication chez cet organisme, et la nécessité de mieux comprendre comment est régulée l’initiation de la réplication en présence comme en absence d’origines de réplication.
• Ultrafast photooxidation of semireduced flavin in fatty acid photodecarboxylase
  
  • Vos Marten
  • Balduzzi Elsa
  • Sorigué Damien
  • Aleksandrov Alexey
  Science Advances, American Association for the Advancement of Science (AAAS), 2025, 11 (38). The initial photoproduct of the natural photoenzyme fatty acid photodecarboxylase involves the flavin anion radical flavin adenine dinucleotide (FAD •– ). Using spectrally resolved ultrafast transient absorption spectroscopy, we demonstrate that FAD •– photoexcitation in the absence of substrate leads to the formation of the oxidized flavin FAD ox (the resting state in the catalytic cycle) within 100 femtoseconds. While this feature is similar to that occurring in flavoprotein oxidases, the ensuing photocycle is more complex. Upon excitation at the lowest-energy transition, the ejected electron is initially captured as a hydrated electron ( e – H ) before transferring to a secondary acceptor in 2.5 picoseconds and returning to the flavin in 37 picoseconds. This implies that e – H can be generated within a protein environment, an unprecedented finding. This assessment is supported by molecular dynamics simulations showing an expansion of the flavin-binding pocket without substrate, allowing water molecules to fill the void. Our results may pave the way to developing unconventional photocatalytic processes. (10.1126/sciadv.adz1904)
  DOI : 10.1126/sciadv.adz1904
• Circular RNAs in Archaea
  
  • Becker Hubert
  • Ferreira-Cerca Sébastien
  , 2025, 1485, pp.451-464. Circular RNA molecules were first described more than 40 years ago. However, it is only recently that the broadness of their phylogenetic distribution has been revealed. Since their discoveries, numerous studies have characterized the molecular mechanisms and function underlying these peculiar molecules, mostly in diverse eukaryotic species. In contrast, studies focusing on the biology of circular RNAs in archaea remain relatively scarce. In this chapter, we provide an overview of the discovery of circular RNAs in archaea and summarize our knowledge of their biology, with an emphasis on circular pre-ribosomal RNAs and Box C/D RNAs. (10.1007/978-981-96-9428-0_26)
  DOI : 10.1007/978-981-96-9428-0_26
• A Selective and Sensitive Method for Colistin Detection by G-Quadruplex Ligand Competition
  
  • Wei Shijiong
  • Qiu Dehui
  • Yan Xinrong
  • Liu Bin
  • Mergny Jean-Louis
  • Monchaud David
  • Ju Huangxian
  • Zhou Jun
  Analytical Chemistry, American Chemical Society, 2025, 97 (31), pp.16805. Colistin (COL) is a widely used antibiotic and is quite often used as a last-resort treatment option for treating multidrug-resistant Gram-negative bacterial infections. Due to its widespread use, COL accumulates in nature, which represents a novel ecological and health threat. However, there is currently no rapid and specific method available for titrating COL levels in collected samples. Herein, we report a simple chemiluminescence detection method based on the specific interaction between COL and a parallel G-quadruplex (G4). To this end, we exploit the catalytic properties of the G4/hemin DNAzyme, which is able to oxidize substrates to provide a readily monitored readout. The stronger affinity of G4 for COL versus hemin allows for the inactivation of the G4/hemin DNAzyme, which is used herein to quantify COL in solution. Through a series of optimizations, we identified the best G4 sequence (F3TC), oxidation substrate (luminol), and experimental conditions, which allow for the detection of COL over a broad concentration window, from 0.5 to 2,500 ng/mL, with a detection limit of 0.4 ng/mL and excellent selectivity against other antibiotics. Compared with existing methods, the proposed approach provides a simpler and label-free quantification of COL, which might serve as a valuable standard method for antibiotic detection, whose use was validated under real conditions herein (10.1021/acs.analchem.5c01733)
  DOI : 10.1021/acs.analchem.5c01733
• Design, synthesis, biophysical and biological evaluation of original condensed pyrrolopyrimidine and pyrrolopyridine ligands as anti-SARS-CoV-2 agents targeting G4
  
  • Guillon Jean
  • Savrimoutou Solène
  • da Rocha Nicolas
  • Albenque-Rubio Sandra
  • Helynck Olivier
  • Durand Cyrielle
  • Chiaravalli Jeanne
  • Pinaud Noël
  • Ronga Luisa
  • Moreau Stéphane
  • Chirold Simon
  • Zangmo Tshering
  • Arab Melika
  • Lari Lindita
  • Mergny Jean‐louis
  • Munier-Lehmann Hélène
  • Lavigne Marc
  European Journal of Medicinal Chemistry, Elsevier, 2025, 292, pp.117655. The design and synthesis of novel bis[(substituted-aminomethyl)phenyl]phenyl pyrrolopyrimidines, pyrrolopyridines, pyrazolopyrimidines, imidazopyrimidines, and tris[(substituted-aminomethyl)phenyl]phenyl pyrrolopyrimidines are reported here. These original G-quadruplex (G4) ligands have been then subjected to a screening on SARS-CoV-2 using a competition HTRF assay by targeting the SUD-NM/TRF2 RNA G4 interaction. The more promising derivatives have been evaluated in vitro to determine their potential antiviral effect on two different cell lines infected by two SARS-CoV-2 strains. This study revealed a clear correlation between their antiviral property and their efficacy to prevent the SUD/G4 interaction. This correlation supports the choice of SUD/RNA G4 complexes formed during SARS-CoV-2 infection as new antiviral targets (10.1016/j.ejmech.2025.117655)
  DOI : 10.1016/j.ejmech.2025.117655
• Chromium‐Doped Zinc Gallate Nanoparticles for Enhanced Enzyme‐Linked Immunosorbent Assay Sensitivity: Optimization of Synthesis and Functionalization Strategies for Ultra‐Low IgG Detection
  
  • Ferjaoui Zied
  • Liu Jianhua
  • Matuszewska Celina
  • Chanéac Corinne
  • Viana Bruno
  • Bouzigues Cédric
  • Scherman Daniel
  • Mignet Nathalie
  • Richard Cyrille
  Small Science, Wiley, 2025, 5 (10). The use of zinc gallate nanoparticles (ZnGa 2 O 4 :Cr 3+ ) (ZGO‐NPs) presents significant potential for improving the sensitivity in enzyme‐linked immunosorbent assays (ELISA). The persistent luminescence signal increase of these nanoparticles in the presence of hydrogen peroxide (H 2 O 2 ) offers advantages for the sensitive detection of biomolecules. Herein, different conditions of ZGO synthesis have been investigated by varying the hydrothermal reaction duration (6, 12, and 24 h) and examining its impact in the presence of H 2 O 2 . These nanoparticles have been integrated into ELISA assays, using as target antigen IgG. The lowest limit of detection (LOD) of 0.2 pg mL −1 is observed for ZGO‐NPs prepared during 12 h (ZGO2), and with a detection range from 1 to 1000 pg mL −1 . The impact of covalently functionalizing these nanoparticles has then been assessed. First using glucose oxidase (GOx) and the detection antibody (Ab D ) linked to PEGylated ZGO‐NPs, named ZGO‐GOx‐Ab D . Alternatively, only the detection antibody is linked to the PEG ZGO‐NPs, named ZGO‐Ab D . The results show a significant lowering of the LOD when using the functionalized ZGO2 NPs and also highlight the impact of the signal amplification by H 2 O 2 . Specifically, when using ZGO2‐GOx‐Ab D incubated with glucose to produce H 2 O 2 , or with ZGO2‐Ab D to which H 2 O 2 was added, the LODs are ≈98 and 56 fg mL −1 respectively, with detection ranges from 0.01 to 100 pg mL −1 . (10.1002/smsc.202500177)
  DOI : 10.1002/smsc.202500177
• Design and biological evaluation of bioinspired Lipidic AlkynylCarbinols for anti-TB drug discovery
  
  • Mehalla Chérine
  • Mefoum Leïla
  • Bouvet Jon
  • Djaout Kamel
  • Joly Etienne
  • Baulard Alain
  • Maraval Valérie
  • Bernardes-Génisson Vania
  • Ballereau Stéphanie
  • Génisson Yves
  • Constant Patricia
  • Marrakchi Hedia
  , 2025.
• Bioinspired Lipids as Leads for Developing New Anti-TB agents with a Unique Mechanism of Action
  
  • Mehalla Chérine
  • Bouvet Jon
  • Mefoum Leïla
  • Stella Alexandre
  • Britton Sébastien
  • Joly Etienne
  • Djaout Kamel
  • Baulard Alain
  • Daffé Mamadou
  • Maraval Valérie
  • Bernardes-Génisson Vania
  • Ballereau Stéphanie
  • Génisson Yves
  • Constant Patricia
  • Marrakchi Hedia
  • Mehalla Chérine
  • Bouvet Jon
  • Mefoum Leïla
  • Stella Alexandre
  • Britton Sébastien
  • Joly Etienne
  • Djaout Kamel
  • Baulard Alain
  • Daffé Mamadou
  • Maraval Valérie
  • Bernardes-Génisson Vania
  • Ballereau Stéphanie
  • Génisson Yves
  • Constant Patricia
  • Marrakchi Hedia
  , 2025.
• In situ determination and matching of the refractive index of the Human cornea to improve polarization-resolved SHG imaging in depth
  
  • Nyembo Kasongo Poncia
  • Mahou Pierre
  • Sintès Jean-Marc
  • Latour Gaël
  • Schanne-Klein Marie-Claire
  Biomedical optics express, Optical Society of America - OSA Publishing, 2025, 16 (8), pp.3270-3282. <div><p>The human cornea is a highly organized tissue, which comprises hundreds of 1-3 µm thick stacked collagen lamellae. However, this microstructure is poorly characterized and requires further investigation. Polarization-resolved second harmonic generation (pSHG) microscopy is a powerful technique for this purpose because of its specificity for collagen and its sensitivity to its orientation. However, pSHG is prone to spatial resolution degradation with depth unless the immersion refractive index is matched to that of the sample, which is critical for corneas that are approximately 600 µm thick. In the absence of experimental data on the refractive index along the entire cornea, we propose a measurement method that applies to the entire cornea directly under the microscope objective. We then use an iodixanol solution to match the refractive index of the immersion medium to that of the cornea. Finally, we carefully characterize the pSHG orientation data obtained under these optimal conditions, and we show that they provide a better resolution along the entire thickness of the cornea and a better determination of the lamellae orientation.</p></div> (10.1364/boe.564209)
  DOI : 10.1364/boe.564209
• Multiscale characterization of myelin distribution with polarized THG microscopy
  
  • Morizet Josephine
  • Olivier Nicolas
  • Aigrot Marie-Stephane
  • Mahou Pierre
  • Martin Elodie
  • Desmazieres Anne
  • Stankoff Bruno
  • Stringari Chiara
  • Beaurepaire Emmanuel
  Optica, Optical Society of America - OSA Publishing, 2025, 12 (7), pp.1122. Myelin is essential for axonal conduction and metabolic support. To better understand its role in health and disease, it is necessary to establish accurate methods for in situ mapping of myelin at scales ranging from submicrometer to centimeters. Third-harmonic generation (THG) microscopy has recently been proposed as an efficient label-free method to visualize myelin in thick and living tissue. However, the contrast mechanism of THG from myelinated axons is complex and poorly described, which has limited the development of THG as a quantitative probe of myelin distribution. Here, we present a systematic characterization and modeling of polarization-resolved THG (pTHG) signals from individual axons as a function of their diameter and myelin thickness, and we show that pTHG can be used to derive myelin scores in several biological systems. First, we confirm the sensitivity and specificity of the THG contrast for myelinated axons in mouse brain tissue and its ability to detect isolated micrometer-sized axons oriented both in-plane and out-of-plane. We then present a detailed characterization of the pTHG contrast of small and large axons in live zebrafish larvae at different developmental stages, and we demonstrate that pTHG detects early axon development in vivo. We show that classical models of coherent multiphoton microscopy fail to reproduce pTHG profiles of axons because they neglect myelin-induced optical aberrations, and we establish a numerical strategy based on finite-difference time-domain calculations that can accurately relate pTHG signal profiles to axonal diameter and myelin thickness. Finally, we illustrate the relevance of pTHG microscopy for characterizing myelin distribution at different scales in fixed mouse and human brain tissue. (10.1364/optica.562091)
  DOI : 10.1364/optica.562091
• Editorial: The metabolic pathways of archaea
  
  • Myllykallio Hannu
  • Qin Wei
  • Berg Ivan
  Frontiers in Microbiology, Frontiers Media, 2025, 16. (10.3389/fmicb.2025.1648560)
  DOI : 10.3389/fmicb.2025.1648560
• Time Delay Distribution and Laser Stability in Arbitrary Detuning Asynchronous Optical Sampling
  
  • Antonucci Laura
  • Bonvalet A.
  • Solinas X.
  • Joffre M.
  Journal of Physical Chemistry A, American Chemical Society, 2025, 129 (27), pp.6121-6132. Arbitrary Detuning ASynchronous OPtical Sampling (ADA-SOPS) is an emerging technique for extending standard pump−probe experiments performed with two femtosecond lasers to multitimescale experiments, which are of great interest for the study of complex systems. Although no specific requirements are needed for laser repetition rates, their ratio determines the achievable delay distribution and therefore is strongly related to the temporal resolution of the technique. We report a detailed theoretical analysis of measurement performances with respect to laser repetition rates, and we validate our model with experimental data. In the case of amplified laser systems, we demonstrate that achieved delays are inherently correlated to the time interval between amplified pulses, which affects the pulse energy and can generate artifacts. Nevertheless, a deep understanding of the origin of such artifacts allows to suggest several compensation strategies, either during data analysis or at the conception of the experimental setup. Finally we present a new algorithm integrated into the ADASOPS device: by selecting pairs of probe pulses having the same elapsed time with respect to the previous pulse, it automatically compensates any effect of energy fluctuation. (10.1021/acs.jpca.5c01853)
  DOI : 10.1021/acs.jpca.5c01853
• IgG detection in human serum employing non-functionalized chromium doped zinc gallate nanoparticles
  
  • Ferjaoui Zied
  • Zimmer Capucine
  • Matuszewska Celina
  • Chanéac Corinne
  • Viana Bruno
  • Bouzigues Cédric
  • Scherman Daniel
  • Mignet Nathalie
  • Richard Cyrille
  Next Nanotechnology, Elsevier, 2025, 8, pp.100199. Chromium-doped zinc gallate (ZnGa2O4:Cr3 +) nanoparticles (ZGO) show promising potential for antigen immunodetection using persistent luminescence, thereby reducing autofluorescence interference. Recently, we have shown that ZGO prepared by hydrothermal treatment at 120°C for 24 h can be used for in vitro biodetection in simple media such as phosphate-buffered saline. In this study, we investigated the effect of the protocol used to synthesize these ZGO nanoparticles, using a hydrothermal treatment at 220°C for different durations (6 h, 12 h, and 24 h), followed by calcination at 500°C. The nanoparticle size determined by transmission electron microscopy after grinding and centrifugation was found to be around 15 nm. The persistent luminescence signal of the ZGO nanoparticles varied with the hydrothermal synthesis conditions. Moreover, in the presence of H2O2, these nanoparticles show a signal enhancement dependent on the hydrothermal duration, with a 12 h treatment showing the highest 8-fold luminescence increase in the presence of H2O2 produced by glucose oxidase mediated glucose degradation. Based on these results, these non-functionalized nanoparticles were successfully used to develop a persistent luminescence-based sandwich immunoassay for autofluorescence-free detection of antigens in undiluted human serum samples, using rabbit IgG as a model antigen. This study highlights the promising potential for biosensing applications of persistent ZGO nanophosphors for IgG detection in a complex medium (undiluted human serum), with a linear range from 1 ng mL−1 to 104 ng mL−1 and a limit of detection of 0.01 ng mL−1. The present optimization of ZGO nanophosphor synthesis offers promising prospects for medical diagnostics due to their increased sensitivity and ability to eliminate autofluorescence interference, as well as their ease of use, since no functionalization of the ZGO NPs is required before use. (10.1016/j.nxnano.2025.100199)
  DOI : 10.1016/j.nxnano.2025.100199
• Etude du rôle de la myosine II dans la migration cellulaire collective au cours de la gastrulation du poisson-zèbre Danio rerio
  
  • Elouin Amélie
  , 2025. La migration collective des cellules, où chaque cellule dépend de ses voisines pour se diriger, est un processus fondamental présent lors du développement embryonnaire, de la cicatrisation et dans certains processus métastatiques. La question de fond de cette thèse est : comment des cellules qui migrent en groupe s’orientent-elles ? Pour y répondre, cette thèse a utilisé un modèle de choix : la gastrulation de poisson-zèbre (Danio rerio). Lors de cette étape clé du développement embryonnaire, une structure dorsale appelée mésoderme axial s’étend vers le pôle animal, conduite par un groupe de cellules appelées polster. Ces cellules migrent en tête, et contribuent à l’allongement de l’embryon. Les travaux précédents ont montré que les cellules de polster sont guidées par leurs cellules suiveuses immédiates et que ce guidage repose sur de la mécanotransduction via l’α-caténine, qui adopte une conformation ouverte, suggérant que des tensions sont exercées entre les cellules du polster. Mais quelle est l’origine de ces tensions ? Cette thèse s’est concentrée sur le rôle de la myosine II non musculaire (myosine II), une protéine motrice bien connue pour générer des tensions intracellulaires. À l’aide de diverses approches techniques, telles que l’inhibition fonctionnelle de la myosine II par des formes dominantes négatives de kinases comme MLCK et ROCK, des traitements pharmacologiques et des transplantations cellulaires, cette thèse a démontré que l’inhibition de la myosine II est nécessaire à l’orientation des cellules de polster de manière non-autonome, c’est-à-dire par l’intermédiaire de ses effets sur les cellules voisines. Parallèlement, l’utilisation d’une lignée transgénique marquant la myosine II, combinée à un système d’imagerie in vitro, et à des ablations laser par microscopie à 2-photons, a révélé un rôle autonome de la myosine II dans la contractilité des protrusions, et en particulier dans le flux rétrograde d’actine. De plus, l’utilisation d’un anticorps sensible à la tension sur l’α-caténine a montré que la myosine II intervient également de manière non-autonome pour mettre sous tension les jonctions adhérentes. Ensemble, ces résultats soutiennent l’idée que les cellules suiveuses orientent les cellules meneuses en exerçant une traction via des protrusions contractiles, dépendantes de la myosine II. Ce mécanisme de guidage, fondé sur les forces exercées par les cellules arrière, permet une coordination efficace des mouvements collectifs sans avoir recours à des gradients chimiques préétablis. Ce travail positionne ainsi la myosine II comme un acteur clé dans la coordination mécanique des migrations collectives, avec des implications non seulement pour le développement embryonnaire, mais aussi pour des contextes pathologiques comme le cancer.
• Laser driven FLASH radiobiology using a high dose and ultra high dose rate single pulse proton source
  
  • Flacco A
  • Bayart E.
  • Romagnani L
  • Cavallone M.
  • de Marzi L.
  • Fouillade C
  • Giaccaglia C.
  • Heinrich S.
  • Lamarre-Jouenne I.
  • Monzac J.
  • Parodi K.
  • Patriarca A
  • Rösch T
  • Schreiber J
  • Tischendorf L
  Scientific Reports, Nature Publishing Group, 2025, 15, pp.16511. Laser-driven proton sources have long been developed with an eye on their potential for medical application to radiation therapy. These sources are compact, versatile, and show peculiar characteristics such as extreme instantaneous dose rates, short duration and broad energy spectrum. Typical temporal modality of laser-driven irradiation, the so-called fast-fractionation, results from the composition of multiple, temporally separated, ultra-short dose fractions. In this paper we present the use of a high-energy laser system for delivering the target dose in a single nanosecond pulse, for ultra-fast irradiation of biological samples. A transport line composed by two permanent-magnet quadrupoles and a scattering system is used to improve the dose profile and to control the delivered dose-per-pulse. A single-shot dosimetry protocol for the broad-spectrum proton source using Monte Carlo simulations was developed. Doses as high as 20 Gy could be delivered in a single shot, lasting less than 10 ns over a 1 cm diameter biological sample, at a dose-rate exceeding 10 9 Gy s -1 . Exploratory application of extreme laser-driven irradiation conditions, falling within the FLASH irradiation protocol, are presented for irradiation in vitro and in vivo. A reduction of radiation-induced oxidative stress in vitro and radiation-induced developmental damage compatible with the onset of FLASH effect were observed in vivo, whereas anti-tumoral efficacy was confirmed by cell survival assay. (10.1038/s41598-025-01105-z)
  DOI : 10.1038/s41598-025-01105-z
• Two-dimensional infrared spectroscopy using a fast-scanning interferometer and chirped pulse up-conversion at 100 kHz
  
  • Jonušas Mindaugas
  • Bournet Quentin
  • Bonvalet Adeline
  • Natile Michele
  • Ersen Andrei-Ovidiu
  • Guichard Florent
  • Zaouter Yoann
  • Georges Patrick
  • Druon Frédéric
  • Hanna Marc
  • Joffre Manuel
  The Journal of Chemical Physics, American Institute of Physics, 2025, 162 (17), pp.174201. We report on a 100-kHz two-dimensional infrared (2DIR) spectrometer in the pump-probe geometry, which we apply to the measurement of the 2DIR spectrum of carboxy-hemoglobin. The probe pulses are spectrally resolved by chirped-pulse upconversion (CPU) using a fast 2048-pixel linescan CMOS camera. The two-pulse pump sequence is generated using a conventional interferometer with a fast-scanning mechanical delay line allowing to achieve a scanning frequency of 2 Hz. The resulting modulation frequency of 3.1 kHz is large enough to shift the relevant signal away from the low-frequency noise of the laser source. The combined use of an interferometer on the pump side and of CPU on the probe side opens the way to an improved spectral resolution in both pump and probe dimensions, as compared to currently-available 100-kHz 2DIR spectrometers based on pulse shapers and Mercury-Cadmium Telluride (MCT) detector arrays. (10.1063/5.0261494)
  DOI : 10.1063/5.0261494
• Genome wide analyses reveal the role of mutator phenotypes in Mycobacterium tuberculosis drug resistance emergence
  
  • Zein-Eddine R.
  • Le Meur Adrien
  • Skouloubris S.
  • Jelsbak L.
  • Refrégier Guislaine
  • Myllykallio Hannu Hannu
  npj Antimicrobials and Resistance, Springer Nature, 2025, 3 (1), pp.35. Antimicrobial combination therapy is widely used to combat Mycobacterium tuberculosis (Mtb), yet resistance rates continue to rise. Mutator strains, with defects in DNA repair genes, drive resistance in other bacterial infections, but their role in Mtb remains unclear. Here, we study the contribution of single nucleotide polymorphisms (SNPs) in DNA Repair, Replication, and Recombination (3 R) genes to Mtb resistance. Through large-scale bioinformatics analysis of 53,589 whole-genomes, we identified 18 novel SNPs in lineages 2 and 4 linked to genotypic drug resistance in 3 R genes, covering 12.5% of clinical isolates with available genome sequences. Notably, a number of the detected SNPs were positively selected during Mtb evolution. Experimental tests showed that mutM, fpgg2, xthA, and nucS mutants had increased the mutation frequency compared to the wild type. Our findings highlight the role of 3 R gene mutations in resistance, emphasizing the need for surveillance to improve early detection and control strategies. (10.1038/s44259-025-00107-1)
  DOI : 10.1038/s44259-025-00107-1
• Caractérisation et suivi physico-chimique du collagène lors de l’altération des parchemins par microscopie multiphoton résolue en polarisation
  
  • Galante Giulia
  , 2025. Le parchemin, issu de peaux animales non tannées, grattées et séchées sous tension, est composé à plus de 80% de collagène fibrillaire. Ce matériau est sensible aux changements importants de température et d’humidité. L’évaluation de l’état de dégradation du parchemin est nécessaire pour sa conservation et préalablement à sa restauration. La microscopie multiphoton, technique d’imagerie tridimensionnelle non-invasive et sans contact permet l’accès à des signaux endogènes dans ce matériau : la génération de second harmonique (SHG), spécifique du collagène fibrillaire, et la fluorescence excitée à 2 photon (2PEF), indiquant la présence de gélatine suite à la dénaturation du collagène. La microscopie SHG peut être résolues en polarisation (P-SHG) pour accéder à l’organisation des fibrilles de collagène dans le tissu. Le but de cette thèse est d’étudier si la dégradation peut être mesurée par deux paramètres multiphoton : le ratio des signaux 2PEF et SHG traduisant la proportion de collagène dégradé versus préservé et le paramètre d’anisotropie ρ, traduisant le désordre des fibrilles. Pour cela, divers types de parchemins sont soumis à divers types de vieillissements artificiels en chaleur sèche ou chaleur humide. Nous avons d’abord étudié le comportement du paramètre d’anisotropie avec l’organisation des fibrilles de collagène dans le parchemin pour déterminer les conditions pour que ce paramètre soit une mesure fiable de dégradation. Nous avons ensuite étudié la dégradation du collagène par microscopie P-SHG en fonction de la durée et de la méthode de vieillissement, en se référant à des mesures de température de dénaturation par DSC. Nous avons observé des différences entre parchemins modernes et anciens, mais aussi réussi à discriminer des dégradations en chaleur sèche et chaleur humide. Enfin des mesures sur des fibres de collagène isolées et sur deux cas d’étude sont décrits.
• Genome-wide ribonucleotide detection in Archaea
  
  • Moalic Yann
  • Reveil Maurane
  • Kundnani Deepali L
  • Balachander Sathya
  • Yang Taehwan
  • Gombolay Alli
  • Ranjbarian Farahnaz
  • Brizard Raphael
  • Durand Patrick
  • Myllykallio Hannu
  • Jebbar Mohamed
  • Hofer Anders
  • Storici Francesca
  • Henneke Ghislaine
  , 2025. ABSTRACT Genome integrity is constantly challenged by the incorporation of ribonucleotides (rNMPs) during DNA synthesis. Covalently linked single and several consecutive rNMPs occur in the genome of a number of organisms. They are mainly introduced by DNA polymerases during DNA replication and repair. In general, cells evolved ribonucleases H (RNases H) specialized in the removal of rNMPs from DNA to avoid any detrimental consequences on genome stability. Here, we describe the involvement of types 1 and/or 2 RNases H in processing embedded rNMPs in the genome of two archaeal species Haloferax volcanii and Thermococcus barophilus . Using combined approaches that include alkaline DNA fragmentation, high-throughput ribose-seq DNA sequencing and nucleotide pool quantification, the distribution, identity, level and sequence context of genomic rNMPs are reported and discussed regards to the intracellular balances of dNTPs and rNTPs. Our results confirm the predominant role of type 2 RNase H in the removal of genomic rNMPs. They also reveal rNMP-base compositions, densities, locations, and variations of surrounding bases at rNMP-embedment for each mutant. The cellular roles of the different RNases H in processing rNMPs in the genome of Archaea are discussed. (10.1101/2025.03.17.643674)
  DOI : 10.1101/2025.03.17.643674
• Ultra-Specific G-Quadruplex–Colistin Interaction for Efficient Transcriptome-Wide G4 Mapping
  
  • Wei Shijiong
  • Zhang Xiaobo
  • Feng Yilong
  • Tao Shentong
  • Qiu Dehui
  • Yan Xinrong
  • Li Guangming
  • Guittat Lionel
  • Zhang Wenli
  • Monchaud David
  • Mergny Jean-Louis
  • Ju Huangxian
  • Zhou Jun
  Journal of the American Chemical Society, American Chemical Society, 2025, 147, pp.9962 - 9971. G-quadruplexes (G4s) are challenging targets for chemical biology interventions, notably because of their dynamic topological polymorphism. We found that the antibiotic smallmolecule colistin (COL) interacts specifically with a single subtype of G4 structures, the so-called parallel G4s. This interaction triggers the aggregation of the G4/COL complexes in a structure-specific manner, which can thus be separated from the bulk solution by centrifugation. This unprecedented mode of affinity-precipitation was exploited here to design the COL-induced RNA G4 precipitation and sequencing (CoRP-seq) protocol, which allows for the assessment of the prevalence of RNA G4s in the transcriptome of human cells in a straightforward manner. CoRP-seq shines by its ultraspecificity, simplicity, and practical convenience, which thus advances G4 mapping further and addresses unmet needs in the field of G4omics. (10.1021/jacs.5c01172)
  DOI : 10.1021/jacs.5c01172