Laboratoire d'optique et biosciences
Laboratoire d'optique et biosciences
Laboratoire d'optique et biosciences

Articles

  • Ultrafast dynamics of the UV-induced electronic relaxation in DNA guanine-thymine dinucleotides: from the Franck-Condon states to the minima of the potential energy surfaces
    • Petropoulos Vasilis
    • Martinez-Fernandez Lara
    • Uboldi Lorenzo
    • Maiuri Margherita
    • Cerullo Giulio
    • Balanikas Evangelos
    • Markovitsi Dimitra
    Physical Chemistry Chemical Physics, Royal Society of Chemistry , 2025 . We study the DNA dinucleotide 5’-dGpdT-3’ (abbreviated as GT) as a model system for the relaxation of the electronic excited states in stacked nucleobases. Quantum chemistry calculations determine the Franck-Condon... (10.1039/D5CP00788G)
    DOI : 10.1039/D5CP00788G
  • Factors Affecting the Population of Excited Charge Transfer States in Adenine/Guanine Dinucleotides: A Joint Computational and Transient Absorption Study
    • Petropoulos Vasilis
    • Martinez-Fernandez Lara
    • Uboldi Lorenzo
    • Maiuri Margherita
    • Cerullo Giulio
    • Balanikas Evangelos
    • Markovitsi Dimitra
    Biomolecules, MDPI , 2024, 14 (12), pp.1548 . There is compelling evidence that the absorption of low-energy UV radiation directly by DNA in solution generates guanine radicals with quantum yields that are strongly dependent on the secondary structure. Key players in this unexpected phenomenon are the photo-induced charge transfer (CT) states, in which an electric charge has been transferred from one nucleobase to another. The present work examines the factors affecting the population of these states during electronic relaxation. It focuses on two dinucleotides with opposite orientation: 5′-dApdG-3′ (AG) and 5′-dGpdA-3′ (GA). Quantum chemistry calculations determine their ground state geometry and the associated Franck–Condon states, map their relaxation pathways leading to excited state minima, and compute their absorption spectra. It has been shown that the most stable conformer is anti-syn for AG and anti-anti for GA. The ground state geometry governs both the excited states populated upon UV photon absorption and the type of excited state minima reached during their relaxation. Their fingerprints are detected in the transient absorption spectra recorded with excitation at 266 nm and a time resolution of 30 fs. Our measurements reveal that in the large majority of dinucleotides, chromophore coupling is already operative in the ground state and that the charge transfer process occurs within ~120 fs. The competition among various relaxation pathways affects the quantum yields of the CT state formation in each dinucleotide, which are estimated to be 0.18 and 0.32 for AG and GA, respectively. (10.3390/biom14121548)
    DOI : 10.3390/biom14121548
  • Archaerhodopsin 3 is an ideal template for the engineering of highly fluorescent optogenetic reporters
    • Herasymenko Krystyna
    • Walisinghe Danushka
    • Konno Masae
    • Barneschi Leonardo
    • de Waele Isabelle
    • Sliwa Michel
    • Inoue Keiichi
    • Olivucci Massimo
    • Haacke Stefan
    Chemical Science, The Royal Society of Chemistry , 2024, 16 (2), pp.761-774 . Archaerhodopsin-3 (AR-3) variants stand out among other rhodopsins in that they display a weak, but voltage-sensitive, near-infrared fluorescence emission. This has led to their application in optogenetics both in cell cultures and small animals. However, in the context of improving the fluorescence characteristics of the next generation of AR-3 reporters, an understanding of their ultrafast light-response in light-adapted conditions, is mandatory. To this end, we present a combined experimental and computational investigation of the excited state dynamics and quantum yields of AR-3 and its DETC and Arch-5 variants. The latter always display a mixture of all-trans/15-anti and 13-cis/15-syn isomers, which leads to a bi-exponential excited state decay. The isomerisation quantum yield is reduced more than 20 times as compared to WT AR-3 and proves that the steady-state fluorescence is induced by a single absorption photon event. In wild-type AR-3, we show that a 300 fs, barrier-less and vibrationally coherent isomerization is driven by an unusual covalent electronic character of its all-trans retinal chromophore leading to a metastable twisted diradical (TIDIR), in clear contrast to the standard charge-transfer scenario established for other microbial rhodopsins. We discuss how the presence of TIDIR makes AR-3 an ideal candidate for the design of variants with a one-photon induced fluorescence possibly reaching the emission quantum yield of the top natural emitter neorhodopsin (NeoR). (10.1039/d4sc05120c)
    DOI : 10.1039/d4sc05120c
  • The Balance Between Shear Flow and Extracellular Matrix in Ovarian Cancer‐on‐Chip
    • Chen Changchong
    • Boché Alphonse
    • Wang Zixu
    • Lopez Elliot
    • Peng Juan
    • Carreiras Franck
    • Schanne-Klein Marie‐claire
    • Chen Yong
    • Lambert Ambroise
    • Aimé Carole
    Advanced Healthcare Materials, Wiley , 2024, 13 (23), pp.2400938 . Ovarian cancer is the most lethal gynecologic cancer in developed countries. In the tumor microenvironment, the extracellular matrix (ECM) and flow shear stress are key players in directing ovarian cancer cells invasion. Artificial ECM models based only on ECM proteins are used to build an ovarian tumor‐on‐chip to decipher the crosstalk between ECM and shear stress on the migratory behavior and cellular heterogeneity of ovarian tumor cells. This work shows that in the shear stress regime of the peritoneal cavity, the ECM plays a major role in driving individual or collective ovarian tumor cells migration. In the presence of basement membrane proteins, migration is more collective than on type I collagen regardless of shear stress. With increasing shear stress, individual cell migration is enhanced; while, no significant impact on collective migration is measured. This highlights the central position that ECM and flow shear stress should hold in in vitro ovarian cancer models to deepen understanding of cellular responses and improve development of ovarian cancer therapeutic platforms. In this frame, adding flow provides significant improvement in biological relevance over the authors’ previous work. Further steps for enhanced clinical relevance require not only multiple cell lines but also patient‐derived cells and sera. (10.1002/adhm.202400938)
    DOI : 10.1002/adhm.202400938
  • Quantitative Assessment of Collagen Remodeling during a Murine Pregnancy
    • Ramella-Roman Jessica C
    • Mahendroo Mala
    • Raoux Clothilde
    • Latour Gaël
    • Schanne-Klein Marie-Claire
    ACS photonics, American Chemical Society , 2024, 11 (9), pp.3536-3544 . <div><p>Uterine cervical remodeling is a fundamental feature of pregnancy, facilitating the delivery of the fetus through the cervical canal. Yet, we still know very little about this process due to the lack of methodologies that can quantitatively and unequivocally pinpoint the changes the cervix undergoes during pregnancy. We utilize polarization-resolved second harmonic generation to visualize the alterations the cervix extracellular matrix, specifically collagen, undergoes during pregnancy with exquisite resolution. This technique provides images of the collagen orientation at the pixel level (0.4 μm) over the entire murine cervical section. They show tight and ordered packing of collagen fibers around the os at the early stage of pregnancy and their disruption at the later stages. Furthermore, we utilize a straightforward statistical analysis to demonstrate the loss of order in the tissue, consistent with the loss of mechanical properties associated with this process. This work provides a deeper understanding of the parturition process and could support research into the cause of pathological or premature birth.</p></div> (10.1021/acsphotonics.4c00337)
    DOI : 10.1021/acsphotonics.4c00337
  • Confinement energy landscape classification reveals membrane receptor nano-organization mechanisms
    • Yu Chao
    • Richly Maximilian
    • Hoang Thi Thuy
    • El Beheiry Mohammed
    • Türkcan Silvan
    • Masson Jean-Baptiste
    • Alexandrou Antigoni
    • Bouzigues Cedric I
    Biophysical Journal, Biophysical Society , 2024, 123 (13), pp.1882-1895 . The cell membrane organization has an essential functional role through the control of membrane receptor confinement in micro- or nanodomains. Several mechanisms have been proposed to account for these properties, although some features have remained controversial, notably the nature, size, and stability of cholesterol- and sphingolipid-rich domains or lipid rafts. Here, we probed the effective energy landscape acting on single-nanoparticle-labeled membrane receptors confined in raft nanodomains— epidermal growth factor receptor (EGFR), Clostridium perfringens ε-toxin receptor (CPεTR), and Clostridium septicum α-toxin receptor (CSαTR)—and compared it with hop-diffusing transferrin receptors. By establishing a new analysis pipeline combining Bayesian inference, decision trees, and clustering approaches, we systematically classified single-protein trajectories according to the type of effective confining energy landscape. This revealed the existence of only two distinct organization modalities: confinement in a quadratic energy landscape for EGFR, CPεTR, and CSαTR (A), and free diffusion in confinement domains resulting from the steric hindrance due to F-actin barriers for transferrin receptor (B). The further characterization of effective confinement energy landscapes by Bayesian inference revealed the role of interactions with the domain environment in cholesterol- and sphingolipid-rich domains with (EGFR) or without (CPεTR and CSαTR) interactions with F-actin to regulate the confinement energy depth. These two distinct mechanisms result in the same organization type (A). We revealed that the apparent domain sizes for these receptor trajectories resulted from Brownian exploration of the energy landscape in a steady-state-like regime at a common effective temperature, independently of the underlying molecular mechanisms. These results highlight that confinement domains may be adequately described as interaction hotspots rather than rafts with abrupt domain boundaries. Altogether, these results support a new model for functional receptor confinement in membrane nanodomains and pave the way to the constitution of an atlas of membrane protein organization. (10.1016/j.bpj.2024.06.001)
    DOI : 10.1016/j.bpj.2024.06.001
  • Angle-Resolved Linear Dichroism to Probe the Organization of Highly Ordered Collagen Biomaterials
    • Krins Natacha
    • Wien Frank
    • Schmeltz Margaux
    • Pérez Javier
    • Dems Dounia
    • Debons Nicolas
    • Laberty-Robert Christel
    • Schanne-Klein Marie-Claire
    • Aimé Carole
    Biomacromolecules, American Chemical Society , 2024, 25 (9), pp.6181-6187 . Controlling the assembly of high-order structures is central to soft-matter and biomaterial engineering. Angle-resolved linear dichroism can probe the ordering of chiral collagen molecules in the dense state. Collagen triple helices were aligned by solvent evaporation. Their ordering gives a strong linear dichroism (LD) that changes sign and intensity with varying sample orientations with respect to the beam linear polarization. Being complementary to circular dichroism, which probes the structure of chiral (bio)molecules, LD can shift from the molecular to the supramolecular scale and from the investigation of the conformation to interactions. Supported by multiphoton microscopy and X-ray scattering, we show that LD provides a straightforward route to probe collagen alignment, determine the packing density, and monitor denaturation. This approach could be adapted to any assembly of chiral (bio)macromolecules, with key advantages in detecting large-scale assemblies with high specificity to aligned and chiral molecules and improved sensitivity compared to conventional techniques. (10.1021/acs.biomac.4c00860)
    DOI : 10.1021/acs.biomac.4c00860
  • Impact of trypsin on cell cytoplasm during detachment of cells studied by terahertz sensing
    • Lordon Blandine
    • Campion Tiffany
    • Gibot Laure
    • Gallot Guilhem
    Biophysical Journal, Biophysical Society , 2024, 123 (16), pp.2476-2483 . Trypsin is a very common enzyme used in cell culture to harvest cells by cleaving the proteins responsible for cell adhesion. However, trypsin also induces undesirable effects on cells, such as altering membrane proteins and the cytoskeleton, changing the composition of the cytoplasm and the cell volume, and even leading to cell death when used improperly. Using attenuated total reflection in the terahertz domain, confocal microscopy, and the propidium iodide test, we quantified in real time the change in cytoplasmic content induced by trypsin proteolysis on Madin-Darby canine kidney epithelial cells. We have observed a cytoplasmic modification from the very first seconds of trypsinization, following the change of cell volume due to mechanical re-equilibrium of the membrane. We found that the cytoplasmic alteration is associated with a transfer of small solutes: electrolytes and metabolites. We also found a very good nonlinear correlation between the side effects monitored by terahertz sensing and the cell height, regardless of the dependence of the cell height on trypsin concentration and exposure time. (10.1016/j.bpj.2024.06.011)
    DOI : 10.1016/j.bpj.2024.06.011
  • A Cost‐Effective Hemin‐Based Artificial Enzyme Allows for Practical Applications
    • Qiu Dehui
    • He Fangni
    • Liu Yuan
    • Zhou Zhaoxi
    • Yang Yuqin
    • Long Zhongwen
    • Chen Qianqian
    • Chen Desheng
    • Wei Shijiong
    • Mao Xuanxiang
    • Zhang Xiaobo
    • Mergny Jean‐louis
    • Monchaud David
    • Ju Huangxian
    • Zhou Jun
    Advanced Science, Wiley Open Access , 2024, 11 (32), pp.2402237 . Abstract Nanomaterials excel in mimicking the structure and function of natural enzymes while being far more interesting in terms of structural stability, functional versatility, recyclability, and large‐scale preparation. Herein, the story assembles hemin, histidine analogs, and G‐quadruplex DNA in a catalytically competent supramolecular assembly referred to as assembly‐activated hemin enzyme (AA‐heminzyme). The catalytic properties of AA‐heminzyme are investigated both in silico (by molecular docking and quantum chemical calculations) and in vitro (notably through a systematic comparison with its natural counterpart horseradish peroxidase, HRP). It is found that this artificial system is not only as efficient as HRP to oxidize various substrates (with a turnover number k cat of 115 s −1) but also more practically convenient (displaying better thermal stability, recoverability, and editability) and more economically viable, with a catalytic cost amounting to &lt;10% of that of HRP. The strategic interest of AA‐heminzyme is further demonstrated for both industrial wastewater remediation and biomarker detection (notably glutathione, for which the cost is decreased by 98% as compared to commercial kits). (10.1002/advs.202402237)
    DOI : 10.1002/advs.202402237
  • G-quadruplex forming motifs in the promoter region of the B-MYB proto-oncogene
    • Miranda André
    • Cucchiarini Anne
    • Esnault Cyril
    • Andrau Jean-Christophe
    • Oliveira Paula
    • Mergny Jean‐louis
    • Cruz Carla
    International Journal of Biological Macromolecules, Elsevier , 2024, 270, pp.132244 . To combat cancer, a comprehensive understanding of the molecular mechanisms and behaviors involved in carcinogenesis is crucial, as tumorigenesis is a complex process influenced by various genetic events and disease hallmarks. The B-MYB gene encodes a transcription factor involved in cell cycle regulation, survival, and differentiation in normal cells. B-MYB can be transformed into an oncogene through mutations, and abnormal expression of B-MYB has been identified in various cancers, including lung cancer, and is associated with poor prognosis. Targeting this oncogene is a promising approach for anti-cancer drug design. B-MYB has been deemed undruggable in previous reports, necessitating the search for novel therapeutic options. In this study, we found that the B-MYB gene promoter contains several G/C rich motifs compatible with G-quadruplex (G4) formation. We investigated and validated the existence of G4 structures in the promoter region of B-MYB, first in vitro using a combination of bioinformatics, biophysical, and biochemical methods, then in cell with the recently developed G4access method. (10.1016/j.ijbiomac.2024.132244)
    DOI : 10.1016/j.ijbiomac.2024.132244
  • Non-random spatial organization of telomeres varies during the cell cycle and requires LAP2 and BAF
    • Keller Debora
    • Stinus Sonia
    • Umlauf David
    • Gourbeyre Edith
    • Biot Eric
    • Olivier Nicolas
    • Mahou Pierre
    • Beaurepaire Emmanuel
    • Andrey Philippe
    • Crabbe Laure
    iScience, Cell Press, Elsevier [2018-....] , 2024, 27 (4), pp.109343 . Spatial genome organization within the nucleus influences major biological processes and is impacted by the configuration of linear chromosomes. Here, we applied 3D spatial statistics and modeling on high-resolution telomere and centromere 3D-structured illumination microscopy images in cancer cells. We found a multi-scale organization of telomeres that dynamically evolved from a mixed clustered-and-regular distribution in early G1 to a purely regular distribution as cells progressed through the cell cycle. In parallel, our analysis revealed two pools of peripheral and internal telomeres, the proportions of which were inverted during the cell cycle. We then conducted a targeted screen using MadID to identify the molecular pathways driving or maintaining telomere anchoring to the nuclear envelope observed in early G1. Lamina-associated polypeptide (LAP) proteins were found transiently localized to telomeres in anaphase, a stage where LAP2α initiates the reformation of the nuclear envelope, and impacted telomere redistribution in the next interphase together with their partner barrier-to-autointegration factor (BAF). (10.1016/j.isci.2024.109343)
    DOI : 10.1016/j.isci.2024.109343
  • Catalytic mechanism of fatty acid photodecarboxylase: on the detection and stability of the initial carbonyloxy radical intermediate
    • Aleksandrov Alexey
    • Bonvalet Adeline
    • Müller Pavel
    • Sorigué Damien
    • Beisson Fred
    • Antonucci Laura
    • Solinas Xavier
    • Joffre Manuel
    • Vos Marten
    Angewandte Chemie International Edition, Wiley-VCH Verlag , 2024, 63 (19), pp.e202401376 . In fatty acid photodecarboxylase (FAP), light‐induced formation of the primary radical product RCOO$^●$ from fatty acid RCOO– occurs in 300 ps, upon which CO2 is released quasi‐immediately. Based on the hypothesis that aliphatic RCOO$^●$ (spectroscopically uncharacterized because unstable) absorbs in the red similarly to aromatic carbonyloxy radicals such as 2,6‑dichlorobenzoyloxy radical (DCB$^●$), much longer‐lived linear RCOO$^●$ has been suggested recently. We performed quantum chemical reaction pathway and spectral calculations. These calculations are in line with the experimental DCB$^●$decarboxylation dynamics and spectral properties and show that in contrast to DCB$^●$, aliphatic RCOO$^●$ radicals a) decarboxylate with a very low energetic barrier and on the timescale of a few ps and b) exhibit little red absorption. A time‐resolved infrared spectroscopy experiment confirms very rapid, &lt;&lt;300 ps RCOO$^●$ decarboxylation in FAP. We argue that this property is required for the observed high quantum yield of hydrocarbons formation by FAP. (10.1002/anie.202401376)
    DOI : 10.1002/anie.202401376
  • Correction of non-random mutational biases along a linear bacterial chromosome by the mismatch repair endonuclease NucS
    • Dagva Oyut
    • Thibessard Annabelle
    • Lorenzi Jean-Noël
    • Labat Victor
    • Piotrowski Emilie
    • Rouhier Nicolas
    • Myllykallio Hannu
    • Leblond Pierre
    • Bertrand Claire
    Nucleic Acids Research, Oxford University Press , 2024, 52 (9), pp.5033-5047 . The linear chromosome of Streptomyces exhibits a highly compartmentalized structure with a conserved central region flanked by variable arms. As double strand break (DSB) repair mechanisms play a crucial role in shaping the genome plasticity of Streptomyces, we investigated the role of EndoMS/NucS, a recently characterized endonuclease involved in a non-canonical mismatch repair (MMR) mechanism in archaea and actinobacteria, that singularly corrects mismatches by creating a DSB. We showed that Streptomyces mutants lacking NucS display a marked colonial phenotype and a drastic increase in spontaneous mutation rate. In vitro biochemical assays revealed that NucS cooperates with the replication clamp to efficiently cleave G/T, G/G and T/T mismatched DNA by producing DSBs. These findings are consistent with the transition-shifted mutational spectrum observed in the mutant strains and reveal that NucS-dependent MMR specific task is to eliminate G/T mismatches generated by the DNA polymerase during replication. Interestingly, our data unveil a crescent-shaped distribution of the transition frequency from the replication origin towards the chromosomal ends, shedding light on a possible link between NucS-mediated DSBs and Streptomyces genome evolution. (10.1093/nar/gkae132)
    DOI : 10.1093/nar/gkae132
  • Modeling and Predicting Second-Harmonic Generation from Protein Molecular Structure
    • Asadipour Bahar
    • Beaurepaire Emmanuel
    • Zhang Xingjian
    • Chessel Anatole
    • Mahou Pierre
    • Supatto Willy
    • Schanne-Klein Marie-Claire
    • Stringari Chiara
    Physical Review X, American Physical Society , 2024, 14 (1), pp.011038 . (10.1103/PhysRevX.14.011038)
    DOI : 10.1103/PhysRevX.14.011038
  • G-quadruplex ligands in cancer therapy: Progress, challenges, and clinical perspectives
    • Figueiredo Joana
    • Mergny Jean-Louis
    • Cruz Carla
    Life Sciences, Elsevier , 2024, 340, pp.122481 . Guanine-rich sequences can form G-quadruplexes (G4) in living cells, making these structures promising anti- cancer targets. Compounds able to recognize these structures have been investigated as potential anticancer drugs; however, no G4 binder has yet been approved in the clinic. Here, we describe G4 ligands structure-activity relationships, in vivo effects as well as clinical trials. Addressing G4 ligand characteristics, targeting challenges, and structure-activity relationships, this review provides insights into the development of potent and selective G4-targeting molecules for therapeutic applications. (10.1016/j.lfs.2024.122481)
    DOI : 10.1016/j.lfs.2024.122481
  • Chirped pulse upconversion for femtosecond mid-infrared spectroscopy at 100 kHz
    • Jonušas Mindaugas
    • Bournet Quentin
    • Bonvalet Adeline
    • Natile Michele
    • Guichard Florent
    • Zaouter Yoann
    • Georges Patrick
    • Druon Frédéric
    • Hanna Marc
    • Joffre Manuel
    Optics Express, Optical Society of America - OSA Publishing , 2024, 32 (5), pp.8020 . We demonstrate that chirped pulse up-conversion (CPU), a method routinely used with systems based on 1-kHz Titanium:Sapphire lasers, can be extended to a repetition rate of 100 kHz with an Ytterbium diode-pumped femtosecond amplifier. Individual mid-infrared spectra can thus be measured directly in the near infrared using a fast CMOS linescan camera. After an appropriate Fourier processing, a spectral resolution of 1.1 cm-1 is reported, currently limited by our spectrometer. Additionally, we demonstrate the application of CPU to a pump-probe measurement of the vibrational relaxation in carboxy-hemoglobin, and we show that the combination of fast scanning and fast acquisition enables a straightforward removal of pump scattering interference. (10.1364/oe.515291)
    DOI : 10.1364/oe.515291
  • Preferential formation of Z-RNA over intercalated motifs in long noncoding RNA
    • Bhatt Uditi
    • Cucchiarini Anne
    • Luo Yu
    • Evans Cameron
    • Mergny Jean-Louis
    • Iyer K. Swaminathan
    • Smith Nicole
    Genome Research, Cold Spring Harbor Laboratory Press , 2024, pp.gr.278236.123 . Secondary structure is a principal determinant of lncRNA function, predominantly regarding scaffold formation and interfaces with target molecules. Noncanonical secondary structures that form in nucleic acids have known roles in regulating gene expression and include G-quadruplexes (G4s), intercalated-motifs (iMs), and R-loops (RLs). In this paper, we utilized computational tools G4-iM Grinder and QmRLFS-finder to predict the formation of each of these structures throughout the lncRNA transcriptome in comparison to protein-coding transcripts. The importance of the predicted structures in lncRNA in biological contexts was assessed by combining our results with publicly available lncRNA tissue expression data followed by pathway analysis. The formation of predicted G4 (pG4) and iM (piM) structures in select lncRNA sequences was determined in vitro using biophysical experiments under near-physiological conditions. We found that the majority of the tested pG4s form highly stable G4 structures and identify many previously unreported G4s in biologically important lncRNAs. In contrast, none of the piM sequences were able to form iM structures, consistent with the idea that RNA is unable to form iMs. These C-rich sequences instead formed Z-RNA structures, which have not been previously observed in regions containing cytosine repeats and represent an interesting and under-explored target for protein-RNA interactions. Our results highlight the prevalence and potential structure-associated functions of noncanonical secondary structures in lncRNA and observe G4 and Z-RNA structure formation in many lncRNA sequences for the first time, furthering understanding of the structure-function relationship in lncRNAs. (10.1101/gr.278236.123)
    DOI : 10.1101/gr.278236.123
  • Maximizing the efficiency of intrapulse difference frequency generation by pulse shaping and recycling
    • Bournet Quentin
    • Jonusas Mindaugas
    • Guichard Florent
    • Natile Michele
    • Zaouter Yoann
    • Joffre Manuel
    • Bonvalet Adeline
    • Druon Fréderic
    • Hanna Marc
    • Georges Patrick
    Applied Physics B - Laser and Optics, Springer Verlag , 2024, 130 (2), pp.33 . <div><p>Intrapulse Difference Frequency Generation (iDFG) is an interesting technique for generating femtosecond pulses in the Mid-Infrared (MIR) range with unique properties such as robust Carrier-Envelope Phase (CEP) stability. However, its efficiency is low compared to other techniques. In this paper, we describe an iDFG system operating within the 4 to 10 µm range that features an original architecture to enhance efficiency. First, we introduce an interesting technique on the generation process. This approach involves polarization and spectral phase shaping techniques on the driving pulse to maximize the number of photons enrolled in the process. Second, we demonstrate that the polarization shaping allows further enhancement of efficiency by recycling the iDFG signal to pump a subsequent optical parametric amplification (OPA) stage. These two concepts and the associated parameters optimization are described into details, and supported by experimental results. Combined with a high-power Yb-fiber-based pump laser, these techniques allow to achieve record efficiencies, and generate µJ-level, fewcycle, tunable, CEP-stable pulses in the MIR at repetition rates above 100 kHz.</p></div> (10.1007/s00340-023-08162-0)
    DOI : 10.1007/s00340-023-08162-0
  • Abundance of G-Quadruplex Forming Sequences in the Hepatitis Delta Virus Genomes
    • Brázda Václav
    • Valková Natália
    • Dobrovolná Michaela
    • Mergny Jean-Louis
    ACS Omega, ACS Publications , 2024, 9, pp.4096-4101 . Hepatitis Delta virus (HDV) is a unique and highly unusual RNA satellite virus that depends on the presence of the hepatitis B virus (HBV) to be infectious. Its single-stranded RNA genome is very compact and variable, consisting of eight major genotypes distributed unequally on various continents. The significance of noncanonical secondary structures in DNA or RNA, such as G-quadruplexes (G4s), is becoming more evident especially for transcription, replication, and translation. G4s are formed from guanine-rich sequences and have been found in most eukaryotic and prokaryotic genomes, as well as viruses. In this study, we analyzed the G-quadruplex propensity of HDV genomes using G4Hunter. In contrast to the HBV virus, which has a G4 density similar to that of the human genome, the HDV virus possesses a significantly higher number of potential quadruplex-forming sequences (PQS) with a density more than four times higher than that of the human genome. This observation suggests a crucial role for G-quadruplexes in HDV, particularly because the tracks with the potential to form G-quadruplexes are well conserved. Furthermore, the high prevalence of the G-quadruplex-forming sequence could represent a promising therapeutic target to control HDV replication. (10.1021/acsomega.3c09288)
    DOI : 10.1021/acsomega.3c09288
  • Understanding the cell fate and behavior of progenitors at the origin of the mouse cardiac mitral valve
    • Farhat Batoul
    • Bordeu Ignacio
    • Jagla Bernd
    • Ibrahim Stéphanie
    • Stefanovic Sonia
    • Blanc Hugo
    • Loulier Karine
    • Simons Benjamin
    • Beaurepaire Emmanuel
    • Livet Jean
    • Pucéat Michel
    Developmental Cell, Elsevier , 2024, 59 (3) . Congenital heart malformations include mitral valve defects, which remain largely unexplained. During embryogenesis, a restricted population of endocardial cells within the atrioventricular canal undergoes an endothelial-to-mesenchymal transition to give rise to mitral valvular cells. However, the identity and fate decisions of these progenitors as well as the behavior and distribution of their derivatives in valve leaflets remain unknown. We used single-cell RNA sequencing (scRNA-seq) of genetically labeled endocardial cells and microdissected mouse embryonic and postnatal mitral valves to characterize the developmental road. We defined the metabolic processes underlying the specification of the progenitors and their contributions to subtypes of valvular cells. Using retrospective multicolor clonal analysis, we describe specific modes of growth and behavior of endocardial cell-derived clones, which build up, in a proper manner, functional valve leaflets. Our data identify how both genetic and metabolic mechanisms specifically drive the fate of a subset of endocardial cells toward their distinct clonal contribution to the formation of the valve. (10.1016/j.devcel.2023.12.006)
    DOI : 10.1016/j.devcel.2023.12.006
  • Daily life in the Open Biologist’s second job, as a Data Curator
    • Scorza Livia C.T.
    • Zieliński Tomasz
    • Kalita Irina
    • Lepore Alessia
    • El Karoui Meriem
    • Millar Andrew J
    Wellcome Open Research, F1000Research , 2024, 9, pp.523 . Background: Data reusability is the driving force of the research data life cycle. However, implementing strategies to generate reusable data from the data creation to the sharing stages is still a significant challenge. Even when datasets supporting a study are publicly shared, the outputs are often incomplete and/or not reusable. The FAIR (Findable, Accessible, Interoperable, Reusable) principles were published as a general guidance to promote data reusability in research, but the practical implementation of FAIR principles in research groups is still falling behind. In biology, the lack of standard practices for a large diversity of data types, data storage and preservation issues, and the lack of familiarity among researchers are some of the main impeding factors to achieve FAIR data. Past literature describes biological curation from the perspective of data resources that aggregate data, often from publications. Methods: Our team works alongside data-generating, experimental researchers so our perspective aligns with publication authors rather than aggregators. We detail the processes for organizing datasets for publication, showcasing practical examples from data curation to data sharing. We also recommend strategies, tools and web resources to maximize data reusability, while maintaining research productivity. Conclusion: We propose a simple approach to address research data management challenges for experimentalists, designed to promote FAIR data sharing. This strategy not only simplifies data management, but also enhances data visibility, recognition and impact, ultimately benefiting the entire scientific community (10.12688/wellcomeopenres.22899.1)
    DOI : 10.12688/wellcomeopenres.22899.1
  • Emerging Functional Connections Between Metabolism and Epigenetic Remodeling in Neural Differentiation
    • Sánchez-Ramírez Edgar
    • Ung Thi Phuong Lien
    • Stringari Chiara
    • Aguilar-Arnal Lorena
    Molecular Neurobiology, Springer , 2024 . Stem cells possess extraordinary capacities for self-renewal and differentiation, making them highly valuable in regenerative medicine. Among these, neural stem cells (NSCs) play a fundamental role in neural development and repair processes. NSC characteristics and fate are intricately regulated by the microenvironment and intracellular signaling. Interestingly, metabolism plays a pivotal role in orchestrating the epigenome dynamics during neural differentiation, facilitating the transition from undifferentiated NSC to specialized neuronal and glial cell types. This intricate interplay between metabolism and the epigenome is essential for precisely regulating gene expression patterns and ensuring proper neural development. This review highlights the mechanisms behind metabolic regulation of NSC fate and their connections with epigenetic regulation to shape transcriptional programs of stemness and neural differentiation. A comprehensive understanding of these molecular gears appears fundamental for translational applications in regenerative medicine and personalized therapies for neurological conditions. (10.1007/s12035-024-04006-w)
    DOI : 10.1007/s12035-024-04006-w
  • In-cell NMR suggests that DNA i-motif levels are strongly depleted in living human cells
    • Víšková Pavlína
    • Ištvánková Eva
    • Ryneš Jan
    • Džatko Šimon
    • Loja Tomáš
    • Živković Martina Lenarčič
    • Rigo Riccardo
    • El-Khoury Roberto
    • Serrano-Chacón Israel
    • Damha Masad J
    • González Carlos
    • Mergny Jean-Louis
    • Foldynová-Trantírková Silvie
    • Trantírek Lukáš
    Nature Communications, Nature Publishing Group , 2024, 15 (1), pp.1992 . I-Motifs (iM) are non-canonical DNA structures potentially forming in the accessible, single-stranded, cytosine-rich genomic regions with regulatory roles. Chromatin, protein interactions, and intracellular properties seem to govern iM formation at sites with i-motif formation propensity (iMFPS) in human cells, yet their specific contributions remain unclear. Using in-cell NMR with oligonucleotide iMFPS models, we monitor iM-associated structural equilibria in asynchronous and cell cycle-synchronized HeLa cells at 37 °C. Our findings show that iMFPS displaying pH<sub>T</sub> &lt; 7 under reference in vitro conditions occur predominantly in unfolded states in cells, while those with pH<sub>T</sub> &gt; 7 appear as a mix of folded and unfolded states depending on the cell cycle phase. Comparing these results with previous data obtained using an iM-specific antibody (iMab) reveals that cell cycle-dependent iM formation has a dual origin, and iM formation concerns only a tiny fraction (possibly 1%) of genomic sites with iM formation propensity. We propose a comprehensive model aligning observations from iMab and in-cell NMR and enabling the identification of iMFPS capable of adopting iM structures under physiological conditions in living human cells. Our results suggest that many iMFPS may have biological roles linked to their unfolded states (10.1038/s41467-024-46221-y)
    DOI : 10.1038/s41467-024-46221-y
  • New 2,4-bis[(substituted-aminomethyl)phenyl]phenylquinazoline and 2,4-bis[(substituted-aminomethyl)phenyl]phenylquinoline derivatives: synthesis and biological evaluation as novel anticancer agents by targeting G-quadruplex
    • Guillon Jean
    • Le Borgne Marc
    • Milano Vittoria
    • Guédin-Beaurepaire Aurore
    • Moreau Stéphane
    • Pinaud Noël
    • Ronga Luisa
    • Savrimoutou Solène
    • Albenque-Rubio Sandra
    • Marchivie Mathieu
    • Kalout Haouraa
    • Walker Charley
    • Chevallier Louise
    • Buré Corinne
    • Largy Eric
    • Gabelica Valérie
    • Mergny Jean-Louis
    • Baylot Virginie
    • Ferrer Jacky
    • Idrissi Yamina
    • Chevret Edith
    • Desplat Vanessa
    • Schelz Zsuzsanna
    • Zupkó István
    Pharmaceuticals, MDPI , 2024, 17 (1), pp.30 . The syntheses of novel 2,4-bis[(substituted-aminomethyl)phenyl]phenylquinazolines 12 and 2,4-bis[(substituted-aminomethyl)phenyl]phenylquinolines 13 are reported here in six steps starting from various halogeno-quinazoline-2,4-(1H,3H)-diones or substituted anilines. The antiproliferative activities of the products were determined in vitro against a panel of breast (MCF-7 and MDA-MB-231), human adherent cervical (HeLa and SiHa), and ovarian (A2780) cell lines. Disubstituted 6- and 7-phenyl-bis(3-dimethylaminopropyl)aminomethylphenyl-quinazolines 12b, 12f, and 12i displayed the most interesting antiproliferative activities against six human cancer cell lines. In the series of quinoline derivatives, 6-phenyl-bis(3-dimethylaminopropyl)aminomethylphenylquinoline 13a proved to be the most active. G-quadruplexes (G4) stacked non-canonical nucleic acid structures found in specific G-rich DNA, or RNA sequences in the human genome are considered as potential targets for the development of anticancer agents. Then, as small aza-organic heterocyclic derivatives are well known to target and stabilize G4 structures, their ability to bind G4 structures have been determined through FRET melting, circular dichroism, and native mass spectrometry assays. Finally, telomerase inhibition ability has been also assessed using the MCF-7 cell line. (10.3390/ph17010030)
    DOI : 10.3390/ph17010030
  • Additive CHARMM Force Field for Pterins and Folates
    • Balduzzi Elsa
    • Yin Wenlu
    • Lambry Jean‐christophe
    • Myllykallio Hannu
    • Aleksandrov Alexey
    Journal of Computational Chemistry, Wiley , 2024, 46 (1) . Folates comprise a crucial class of biologically active compounds related to folic acid, playing a vital role in numerous enzymatic reactions. One-carbon metabolism, facilitated by the folate cofactor, supports numerous physiological processes, including biosynthesis, amino acid homeostasis, epigenetic maintenance, and redox defense. Folates share a common pterin heterocyclic ring structure capable of undergoing redox reactions and existing in various protonation states. This study aimed to derive molecular mechanics parameters compatible with the CHARMM36 all-atom additive force field for pterins and biologically important folates, including pterin, biopterin, and folic acid. Three redox forms were considered: oxidized, dihydrofolate, and tetrahydrofolate states. Across all protonation states, a total of 18 folates were parameterized. Partial charges were derived using the CHARMM force field parametrization protocol, based on targeting reference quantum mechanics monohydrate interactions, electrostatic potential, and dipole moment. Bonded terms were parameterized using one-dimensional adiabatic potential energy surface scans, and two-dimensional scans to parametrize in-ring torsions associated with the puckering states of dihydropterin and tetrahydropterin. The quality of the model was demonstrated through simulations of three protein complexes using optimized and initial parameters. These simulations underscored the significantly enhanced performance of the folate model developed in this study compared to the initial model without optimization in reproducing structural properties of folate-protein complexes. Overall, the presented molecular mechanics model will be valuable for modeling folates in various redox states and serve as a staring point for parameterizing other folate derivatives. (10.1002/jcc.27548)
    DOI : 10.1002/jcc.27548