Project publications (contract# ANR-11-EQPX-0029)

Research articles
2021
Cell Stem Cell (2021) Dray et al. https://doi.org/10.1016/j.stem.2021.03.014
Dynamic spatiotemporal coordination of neural stem cell fate decisions through local feedback in the adult vertebrate brain
Science Advances (2021) Schmeltz et al. https://doi.org/10.1126/sciadv.abg1090
Noninvasive quantitative assessment of collagen degradation in parchments by polarization-resolved SHG microscopy
Science Advances (2021) Fokin et al.https://doi.org/10.1126/sciadv.abd5956
The Arp1/11 Minifilament of Dynactin primes the Endosomal Arp2/3 Complex
Nature Commun (2021) Benaissa et al. https://doi.org/10.1038/s41467-021-27334-0
Engineering of a fluorescent chemogenetic reporter with tunable color for advanced live-cell imaging
PNAS (2021) Johnson et al. https://doi.org/10.1073/pnas.2113046118
The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis
Optica (2021) Morizet et al. https://doi.org/10.1364/OPTICA.421257
Modeling nonlinear microscopy near index-mismatched interfaces
Nanoscale (2021) Mousseau et al. https://doi.org/10.1039/D1NR03358A
Luminescent lanthanide nanoparticle-based imaging enables ultra-sensitive, quantitative and multiplexed in vitro lateral flow immunoassays
ACS Sensors (2021) Adelizzi et al. https://doi.org/10.1021/acssensors.0c02414
Quantitative Model for Reversibly Photoswitchable Sensors
Glia (2021) Belmaati et al. https://doi.org/10.1002/glia.23941
Dp71 contribution to the molecular scaffold anchoring aquaporine-4 channels in brain macroglial cells
mBio (2021) Nicoud et al. https://doi.org/10.1128/mBio.00895-21
Sinorhizobium meliloti Functions Required for Resistance to Antimicrobial NCR Peptides and Bacteroid Differentiation
Biomolecules (2021) Busset et al. https://doi.org/10.3390/biom11111592
The Type III Effectome of the Symbiotic Bradyrhizobium vignae Strain ORS3257
J Phys Chem Lett (2021) Hamon et al. https://doi.org/10.1021/acs.jpclett.1c01311
Doping Liquid Crystals of Colloidal Inorganic Nanotubes by Additive-Free Metal Nanoparticles
mSystems (2021) diCenzo et al. https://doi.org/10.1128/mSystems.01092-21
DNA Methylation in Ensifer Species during Free-Living Growth and during Nitrogen-Fixing Symbiosis with Medicago spp
Int J Pharmaceutics (2021) Gürcan et al. https://doi.org/10.1016/j.ijpharm.2021.120381
Combining dexamethasone and TNF-α siRNA within the same nanoparticles to enhance anti-inflammatory effect
Int J Pharmaceutics (2021) Canioni et al. https://doi.org/10.1016/j.ijpharm.2021.120509
Tiny dexamethasone palmitate nanoparticles for intravitreal injection: Optimization and in vivo evaluation
Int J Pharmaceutics (2021) Bourguignon et al. https://dx.doi.org/10.1016/j.ijpharm.2021.121202
An original methodology to study polymeric nanoparticle-macrophage interactions: Nanoparticle tracking analysis in cell culture media and quantification of the internalized objects
Sci Rep (2021) Ung et al. https://doi.org/10.1038/s41598-021-00126-8
Simultaneous NAD(P)H and FAD fluorescence lifetime microscopy of long UVA–induced metabolic stress in reconstructed human
Front Bioeng Biotech (2021) Maury et al. https://doi.org/10.3389/fbioe.2021.574035
Rapid evaluation of novel therapeutic strategies using a 3D collagen-based tissue-like model
Biomed Opt Express (2021) Raoux et al. https://doi.org/10.1364/BOE.426145
Quantitative structural imaging of keratoconic corneas using polarization-resolved SHG microscopy
Int J Mol Sci (2021) Dauplais et al. https://doi.org/10.3390/ijms22115467
Exposure to the Methylselenol Precursor Dimethyldiselenide Induces a Reductive Endoplasmic Reticulum Stress in Saccharomyces cerevisiae
Int J Mol Sci (2021) Simanov et al. https://doi.org/10.3390/ijms22084115
Arpin Regulates Migration Persistence by Interacting with Both Tankyrases and the Arp2/3 Complex
J Neuropathol Exp Neurol (2021) Bouman et al. https://dx.doi.org/10.1093/jnen/nlab012
NEM6, KBTBD13-Related Congenital Myopathy: Myopathological Analysis in 18 Dutch Patients Reveals Ring Rods Fibers, Cores, Nuclear Clumps, and Granulo-Filamentous Protein Material
JoVE (2021) Boutillon et al. https://dx.doi.org/10.3791/62815
Deep and Spatially Controlled Volume Ablations using a Two-Photon Microscope in the Zebrafish Gastrula
ACS Biomat Sci Eng (2021) Picaut et al. https://dx.doi.org/10.1021/acsbiomaterials.0c01273
Core-shell pure collagen threads extruded from highly concentrated solutions promote colonization and differentiation of C3H10T1/2 cells
2020
Science (2020) Guignard et al. https://dx.doi.org/10.1126/science.aar5663
Contact area–dependent cell communication and the morphological invariance of ascidian embryogenesis
Science Advances (2020) Than-Trong et al. https://doi.org/10.1126/sciadv.aaz5424
Lineage hierarchies and stochasticity ensure the long-term maintenance of adult neural stem cells
Nucleic Acids Research (2020) Dardaillon et al. https://doi.org/10.1093/nar/gkz955
ANISEED 2019: 4D exploration of genetic data for an extended range of tunicates
Optica (2020) Schmeltz et al. https://doi.org/10.1364/OPTICA.399246
Circular dichroism-SHG microscopy probes the polarity distribution of collagen fibrils
Chem Sci (2020) Chouket et al. https://doi.org/10.1039/D0SC00182A
Dynamic contrast with reversibly photoswitchable fluorescent labels for imaging living cells
PLoS Biology (2020) Gogendeau et al. https://doi.org/10.1371/journal.pbio.3000640
MKS-NPHP module proteins control ciliary shedding at the transition zone
ACS Photonics (2020) Malkinson et al. https://doi.org/10.1021/acsphotonics.9b01749
Fast in vivo imaging of SHG nanoprobes with multiphoton light-sheet microscopy
ACS Appl Bio Mat (2020) Dems et al. https://doi.org/10.1021/acsabm.0c00006
Native collagen: electrospinning of pure, cross-linker-free, self-supported membrane
BBRC (2020) Brasseur et al. https://doi.org/10.1016/j.bbrc.2020.03.108
Dipeptide repeat derived from C9orf72 hexanucleotide expansions forms amyloids or natively unfolded structures in vitro
Arch Virol (2020) Essoh et al. https://doi.org/10.1007/s00705-019-04511-7
Characterization of 16 Achromobacter xylosoxidans phages from Abidjan, Côte d’Ivoire, isolated on a single clinical strain
Anal Chem (2020) Valanciunaite et al https://doi.org/10.1021/acs.analchem.0c00023
Polarity Mapping of Cells and Embryos by Improved Fluorescent Solvatochromic Pyrene Probe
Plant J (2020) Magne et al. https://doi.org/10.1111/tpj.14758
Roles of BdUNICULME4 and BdLAXATUM‐A in the non‐domesticated grass Brachypodium distachyon
Front Cell Dev Biol (2020) Joly et al. https://doi.org/10.3389/fcell.2020.608600
Membrane Dynamics and Organization of the Phagocyte NADPH Oxidase in PLB-985 Cells
BCP (2020) Song et al. https://doi.org/10.1016/j.bcp.2020.114088
Class I phosphoinositide 3-kinases control sustained NADPH oxidase activation in adherent neutrophils
Int J Mol Sci (2020) Bakayan et al. https://doi.org/10.3390/ijms21217846
RedquorinXS Mutants with Enhanced Calcium Sensitivity and Bioluminescence Output Efficiently Report Cellular and Neuronal Network Activities
Int J Pharm (2020) Qiu et al. https://doi.org/10.1016/j.ijpharm.2020.119281
Self-assembled multifunctional core–shell highly porous metal–organic framework nanoparticles
Nanomaterials (2020) Nedder et al. https://doi.org/10.3390/nano10071309
Uptake of Cerium Dioxide Nanoparticles and Impact on Viability, Differentiation and Functions of Primary Trophoblast Cells from Human Placenta
Mol Microbiol (2020) Kabani et al. https://doi.org/10.1111/mmi.14515
Glucose availability dictates the export of the soluble and prion forms of Sup35p via periplasmic or extracellular vesicles
J Phys: Photonics (2020) Chouket et al. https://iopscience.iop.org/article/10.1088/2515-7647/ab9099
Dynamic contrast for plant phenotyping
BBRC (2020) Kabani et al. https://doi.org/10.1016/j.bbrc.2020.06.024
The Yarrowia lipolytica orthologs of Sup35p assemble into thioflavin T-negative amyloid fibrils
F1000Research (2020) Phan & Chessel. https://doi.org/10.12688/f1000research.27395.1
GeNePy3D: a quantitative geometry python toolbox for large scale bioimaging
J Microsc (2020) Boulogne et al. https://doi.org/10.1111/jmi.12957
Functional organisation of the endomembrane network in the digestive gland of the Venus flytrap: revisiting an old story with a new microscopy toolbox
J Phys: Photonics (2020) Chouket et al. https://iopscience.iop.org/article/10.1088/2515-7647/ab9099
Dynamic contrast for overcoming spectral interferences in fluorescence imaging
2019
Nature (2019) Lardennois et al. https://doi.org/10.1038/s41586-019-1509-4
An actin-based viscoplastic lock ensures progressive body-axis elongation
Nature Communications (2019) Clavreul et al. https://doi.org/10.1038/s41467-019-12791-5
Cortical astrocytes develop in a plastic manner at both clonal and cellular levels
Nature Communications (2019) Abdeladim et al. doi:10.1038/s41467-019-09552-9
Multicolor multiscale brain imaging with chromatic multiphoton serial microscopy
Nature Communications (2019) Tebo et al. https://doi.org/10.1038/s41467-019-10855-0
A split fluorescent reporter with rapid and reversible complementation
Nature Communications (2019) Leggio et al. https://doi.org/10.1038/s41467-019-10668-1
MorphoNet: an interactive online morphological browser to explore complex multi-scale data
Optica 6 (2019) Morizet et al. doi:10.1364/OPTICA.6.000385
High-speed polarization-resolved third-harmonic microscopy
Optica 6 (2019) Zhang et al. https://doi.org/10.1364/OPTICA.6.000972
Simple imaging protocol for autofluorescence elimination and optical sectioning in fluorescence endomicroscopy
Front Immunol (2019) Paalme et al. https://doi.org/10.3389/fimmu.2019.02074
Human peripheral blood eosinophils express high levels of the purinergic receptor P2X4
J Biophotonics (2019) Ducourthial et al. https://doi.org/10.1002/jbio.201800336
Monitoring dynamic collagen reorganization during skin stretching with fast polarization‐resolved SHG imaging
Optics Express (2019) Schmeltz et al. https://doi.org/10.1364/OE.27.022685
Implementation of artifact-free circular dichroism SHG imaging of collagen
Chem Comm (2019) Lesur et al. https://doi.org/10.1039/C9CC05754D
First access to a mycolic acid-based bioorthogonal reporter for the study of the mycomembrane and mycoloyltransferases in Corynebacteria
J R Soc Interface (2019) Natale et al. https://doi.org/10.1098/rsif.2019.0263
Implementation of artifact-free circular dichroism SHG imaging of collagen
PLoS ONE 14 (2019) Genthial et al. https://doi.org/10.1371/journal.pone.0209079
THG imaging and analysis of the effect of low gravity on the lacuno-canalicular network of mouse bone
Phys Biol (2019) Diaz Simões et al. https://doi.org/10.1088/1478-3975/aaf92d
Brownian-like deviation of neighboring cells in the early embryogenesis of the zebrafish
Rev Sci Instrum (2019) Mabey et al. https://doi.org/10.1063/1.5092265
Characterization of high spatial resolution lithium fluoride X-ray detectors
2018
Light: Science & Applications 7 (2018). Zhang et al. doi:10.1038/s41377-018-0098-6
Macroscale fluorescence imaging against autofluorescence under ambient light
Light: Science & Applications 7 (2018). Guesmi et al. doi:10.1038/s41377-018-0012-2
Dual-color deep-tissue three-photon microscopy with a multiband infrared laser
Cell Reports 25 (2018). Ferreira et al. doi:doi.org/10.1016/j.celrep.2018.10.069
Chiral Cilia Orientation in the Left-Right Organizer
Development 145 (2018). Fabrèges et al. doi:doi.org/10.1242/dev.152041
Control of the proportion of inner cells by asymmetric divisions and the ensuing resilience of cloned rabbit embryos
Nucleic Acids Research 46 (2018). Brozovic et al. doi:10.1093/nar/gkx1108
ANISEED 2017: extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets
Nucleic Acids Research 46 (2018). Delpech et al. doi:10.1093/nar/gky829
Snapshots of archaeal DNA replication and repair in living cells using super-resolution imaging
EMBO J (2018). Visweshwaran et al. https://doi.org/10.15252/embj.201797706
The trimeric coiled‐coil HSBP 1 protein promotes WASH complex assembly at centrosomes
Biomaterials Science 27 (2018). Tidu et al. doi:10.1039/c7bm01163f.
Highly concentrated collagen solutions leading to transparent scaffolds of controlled 3D organizations for corneal epithelial cell colonization
Scientific Reports 8 (2018). Faenov et al. doi:10.1038/s41598-018-34717-9
Advanced high resolution x-ray diagnostic for HEDP experiments
2017
Current Biology 27 (2017). Furlan et al. doi:10.1016/j.cub.2017.09.052
Life-long neurogenic activity of individual neural stem cells and continuous growth establish an outside-in architecture in the teleost pallium
eLife 6:e25078 (2017). Ferreira et al. doi:10.7554/eLife.25078
Physical limits of flow sensing in the left-right organizer
eLife 6:e22268 (2017). Dyballa et al. doi:10.7554/eLife.22268
Distribution of neurosensory progenitor pools during inner ear morphogenesis unveiled by cell lineage reconstruction
Nature Commun. 8, 13929 (2017). Delile et al. doi:10.1038/ncomms13929
A cell-based computational model of early embryogenesis coupling mechanical behaviour and gene regulation
Small 13, 1701442 (2017). Mahou et al. doi:10.1002/smll.201701442
Metrology of multiphoton microscopes using second harmonic generation nanoprobes
Opt. Lett. 42 (2017). Burcklen et al. doi:10.1364/OL.42.001927
High-reflectance magnetron-sputtered scandium-based x-ray multilayer mirrors for the water window
Langmuir 27 (2017). Portier et al. doi:10.1021/acs.langmuir.7b02142
Stabilization of collagen fibrils by gelatin addition: A study of collagen/gelatin dense phases
Scientific Reports 7, 3792 (2017). Stringari et al. doi:10.1038/s41598-017-03359-8
Multicolor two-photon imaging of endogenous fluorophores in living tissues by wavelength mixing
Scientific Reports 7, 3419 (2017). Genthial et al. doi:10.1038/s41598-017-03548-5
Label-free imaging of bone multiscale porosity and interfaces using third-harmonic generation microscopy
Chem. Sci. (2017). Li et al. doi:10.1039/C7SC01364G
Dynamic multicolor protein labeling in living cells
J. Optics 19, 065506 (2017). Cadroas et al. doi:10.1088/2040-8986/aa6f72
All-fiber femtosecond laser providing 9 nJ, 50 MHz pulses at 1650 nm for three-photon microscopy
2016
Nature Commun. 7, 8674 (2016). Faure et al. doi:10.1038/ncomms9674
A workflow to process 3D+time microscopy images of developing organisms and reconstruct their cell lineage
Scientific Reports 6, 29863 (2016). Vuillemin et al. doi:10.1038/srep29863
Efficient second-harmonic imaging of collagen histological slides using Bessel beam excitation
Scientific Reports 6, 26344 (2016). Latour et al. doi:10.1038/srep26344
Correlative nonlinear optical microscopy and infrared nanoscopy reveals collagen degradation in altered parchments
Opt. Express 24, 16084 (2016). Teulon et al. doi:10.1364/OE.24.016084
Probing the 3D structure of cornea-like collagen liquid crystals with polarization-resolved SHG microscopy
J. Appl. Phys. 119, 125307 (2016). Burcklen et al. doi:10.1063/1.4944723
Efficient Cr/B4C multilayer mirrors: Study of interfaces and X-ray reflectance
ChemPhysChem (2016). Querard et al. doi:10.1002/cphc.201500987
Kinetics of reactive modules adds discriminative dimensions for selective cell imaging
Org Biomol Chem (2016). Li et al. doi:10.1039/c6ob01612j
Design and characterization of red fluorogenic push–pull chromophores holding great potential for bioimaging and biosensing
2015
Nature Methods 12, 379-80 (2015). Wolf et al. doi:10.1038/nmeth.3371
Whole-brain functional imaging with two-photon light-sheet microscopy
Development 142, 3592-3600 (2015). Dray et al. doi:0.1242/dev.123018
Large-scale live imaging of adult neural stem cells in their endogenous niche
ACS Chem. Biol. 10, 1643-1647 (2015). Delacour et al. doi: 10.1021/acschembio.5b00069
Light-Activated Proteolysis for the Spatiotemporal Control of Proteins.
Angew Chem Int Ed. 54(9):2633-2637 (2015). Querard et al. doi: 10.1002/anie.201408985
Photoswitching Kinetics and Phase-Sensitive Detection Add Discriminative Dimensions for Selective Fluorescence Imaging
PNAS (2015). Plamont et al. doi:10.1073/pnas.1513094113
Small fluorescence-activating and absorption-shifting tag for tunable protein imaging in vivo
Chem. Sci. 6(5):2968-2978 (2015). Querard et al. doi: 10.1039/C4SC03955F
Expanding discriminative dimensions for analysis and imaging
2014
Nature Methods 11, 600-1 (2014). Mahou et al. doi:10.1038/nmeth.2963
Multicolor two-photon light-sheet microscopy
PLoS ONE 9, e104250 (2014). Débarre et al. doi:10.1371/journal.pone.0104250
Mitigating phototoxicity during multiphoton microscopy of live Drosophila embryos in the 1.0–1.2 µm wavelength range
 
 
Reviews and proceedings
Meth Mol Biol (2021) Chouket et al. https://doi.org/10.1007/978-1-0716-1593-5_13
Out-of-Phase Imaging after Optical Modulation (OPIOM) for Multiplexed Fluorescence Imaging Under Adverse Optical Conditions
Chem Sci (2020) Chouket et al.
Dynamic contrast with reversibly photoswitchable fluorescent labels for imaging living cells
Meth Mol Biol (2019) Bancelin et al.
Combination of Traction Assays and Multiphoton Imaging to Quantify Skin Biomechanics
IEEE ISBI (2019) Phan et al.
Automated Quantification With Sub-Micrometer Scale Precision In Volumetric Multicolor Multiphoton Microscopy Images
IEEE ICIP (2018). Nourbakhsh et al.
Neural cell segmentation in large-scale 3D color fluorescence microscopy images for developmental neuroscience
Photochem. Photobiol. (2017). Bakayan et al. doi:10.1111/php.12682
Fluorescent Protein–photoprotein Fusions and Their Applications in Calcium Imaging
Methods Appl. Fluoresc. 3(4):042007 (2015). Jullien & Gautier. doi:10.1088/2050-6120/3/4/042007
Fluorogen-based reporters for fluorescence imaging: a review
Proc.SPIE 9329Z (2015). Mahou et al. doi:10.1117/12.2079176
Multiphoton light-sheet microscopy using wavelength mixing: fast multicolor imaging of the beating Zebrafish heart with low photobleaching
Angew Reviews (2015). Alouane et al.
Self-immolative spacers: kinetic aspects, structure-property relationships, and applications
Nat Chem Biol (2014). Gautier et al.
How to control proteins with light in living systems
 
 
Some previous references from developing partners
Nat Rev Mol Cell Biol 2014. Pantazis & Supatto. Advances in whole-embryo imaging: a quantitative transition is underway.
Nat Commun 2014. Bancelin et al. Determination of collagen fibril size via absolute measurements of second-harmonic generation signals.
Neuron 2014. Loulier et al. Multiplex cell and lineage tracking with combinatorial labels.
Phys Rev X 2013. Zimmerley et al. Probing ordered lipid assemblies with polarized third-harmonic-generation microscopy.
Nat Meth 2012. Mahou et al. Multicolor two-photon tissue imaging by wavelength mixing.
Nat Meth 2011. Truong et al. Deep and fast live imaging with two-photon scanned light-sheet microscopy.
Science 2010. Olivier et al. Cell Lineage Reconstruction of Early Zebrafish Embryos Using Label-Free Nonlinear Microscopy.