ENS - Départment de biologie

Fast wavefront shaping for two-photon brain imaging with multipatch correction.

Frédérique Godfroid — 2023-12-19T16:08:34Z

Abstract

Nonlinear fluorescence microscopy promotes in-vivo optical imaging of cellular structure at diffraction-limited resolution deep inside scattering biological tissues. Active compensation of tissue-induced aberrations and light scattering through adaptive wavefront correction further extends the accessible depth by restoring high resolution at large depth. However, those corrections are only valid over a very limited field of view within the angular memory effect. To overcome this limitation, we introduce an acousto-optic light modulation technique for fluorescence imaging with simultaneous wavefront correction at pixel scan speed. Biaxial wavefront corrections are first learned by adaptive optimization at multiple locations in the image field. During image acquisition, the learned corrections are then switched on the fly according to the position of the excitation focus during the raster scan. The proposed microscope is applied to in vivo transcranial neuron imaging and demonstrates multi-patch correction of thinned skull-induced aberrations and scattering at 40-kHz data acquisition speed.

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Proc Natl Acad Sci U S A. 2023 Dec 19 ;120(51):e2305593120.
doi : 10.1073/pnas.2305593120.

Hypometabolism to survive the long polar night and subsequent successful return to light in the diatom Fragilariopsis cylindrus

Frédérique Godfroid — 2023-12-18T14:10:55Z

Authors
Nathalie Joli, Lorenzo Concia, Karel Mocaer, Julie Guterman, Juliette Laude, Sebastien Guerin, Theo Sciandra, Flavienne Bruyant, Ouardia Ait-Mohamed, Marine Beguin, Marie-Helene Forget, Clara Bourbousse, Thomas Lacour, Benjamin Bailleul, Charlotte Nef, Mireille Savoie, Jean-Eric Tremblay, Douglas A. Campbell, Johann Lavaud, Yannick Schwab, Marcel Babin, Chris Bowler

Summary

• Diatoms, the main eukaryotic phytoplankton of the polar marine regions, are essential for the maintenance of food chains specific to Arctic and Antarctic ecosystems, and are experiencing major disturbances under current climate change. As such, it is fundamental to understand the physiological mechanisms and associated molecular basis of their endurance during the long polar night.
• Here, using the polar diatom Fragilariopsis cylindrus, we report an integrative analysis combining transcriptomic, microscopic and biochemical approaches to shed light on the strategies used to survive the polar night.
• We reveal that in prolonged darkness, diatom cells enter a state of quiescence with reduced metabolic and transcriptional activity, during which no cell division occurs. We propose that minimal energy is provided by respiration and degradation of protein, carbohydrate and lipid stores and that homeostasis is maintained by autophagy in prolonged darkness. We also report internal structural changes that manifest the morphological acclimation of cells to darkness, including the appearance of a large vacuole.
• Our results further show that immediately following a return to light, diatom cells are able to use photoprotective mechanisms and rapidly resume photosynthesis, demonstrating the remarkable robustness of polar diatoms to prolonged darkness at low temperature.

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New Phytol. 2023 Dec 14. doi : 10.1111/nph.19387

GluD1 binds GABA and controls inhibitory plasticity

Frédérique Godfroid — 2023-12-12T21:31:19Z

Abstract

Fast synaptic neurotransmission in the vertebrate central nervous system relies primarily on ionotropic glutamate receptors (iGluRs), that drive neuronal excitation, and type A γ-aminobutyric acid receptors (GABAARs), responsible for neuronal inhibition. However, the GluD1 receptor, an iGluR family member, is present at both excitatory and inhibitory synapses. Whether and how GluD1 activation may impact inhibitory neurotransmission is unknown. Here, using a combination of biochemical, structural and functional analyses, we demonstrate that GluD1 binds GABA, an unprecedented feature for iGluRs. GluD1 activation produces long-lasting enhancement of GABAergic synaptic currents in the adult mouse hippocampus through a non-ionotropic mechanism dependent on trans-synaptic anchoring. The identification of GluD1 as a GABA receptor that controls inhibitory synaptic plasticity challenges the classical dichotomy between glutamatergic and GABAergic receptors.

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Science, 2023, Dec 7:eadf3406. doi : 10.1126/science.adf3406

Choroid plexuses carry nodal-like cilia that undergo axoneme regression from early adult stage

Frédérique Godfroid — 2023-12-08T11:11:40Z

Authors
Kim Hoa Ho, Adrien Candat, Valentina Scarpetta, Marion Faucourt, Solene Weill, Chiara Salio, Elisa D'Este, Martin Meschkat, Christian A Wurm, Matthias Kneussel, Carsten Janke, Maria M Magiera, Auguste Genovesio, Alice Meunier, Marco Sassoè-Pognetto, Monika S Brill, Nathalie Spassky, Annarita Patrizi.

Abstract

Choroid plexuses (ChPs) produce cerebrospinal fluid and sense non-cell-autonomous stimuli to control the homeostasis of the central nervous system. They are mainly composed of epithelial multiciliated cells, whose development and function are still controversial. We have thus characterized the stepwise order of mammalian ChP epithelia cilia formation using a combination of super-resolution-microscopy approaches and mouse genetics. We show that ChP ciliated cells are built embryonically on a treadmill of spatiotemporally regulated events, starting with atypical centriole amplification and ending with the construction of nodal-like 9+0 cilia, characterized by both primary and motile features. ChP cilia undergo axoneme resorption at early postnatal stages through a microtubule destabilization process controlled by the microtubule-severing enzyme spastin and mitigated by polyglutamylation levels. Notably, this phenotype is preserved in humans, suggesting a conserved ciliary resorption mechanism in mammals.
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Dev Cell. 2023 Dec 4 ;58(23):2641-2651.e6. doi : 10.1016/j.devcel.2023.10.003.

Histone H1 protects telomeric repeats from H3K27me3 invasion in Arabidopsis

Frédérique Godfroid — 2023-11-17T18:45:09Z

Authors :
Gianluca Teano^#, Lorenzo Concia^#, Léa Wolff, Léopold Carron, Ivona Biocanin, Kateřina Adamusová, Miloslava Fojtová, Michael Bourge, Amira Kramdi, Vincent Colot, Ueli Grossniklaus, Chris Bowler, Célia Baroux, Alessandra Carbone, Aline V. Probst, Petra Procházková Schrumpfová, Jiří Fajkus, Simon Amiard, Stefan Grob, Clara Bourbousse and Fredy Barneche.

Abstract

While the pivotal role of linker histone H1 in shaping nucleosome organization is well established, its functional interplays with chromatin factors along the epigenome are just starting to emerge. Here we show that, in Arabidopsis, as in mammals, H1 occupies Polycomb Repressive Complex 2 (PRC2) target genes where it favors chromatin condensation and H3K27me3 deposition. We further show that, contrasting with its conserved function in PRC2 activation at genes, H1 selectively prevents H3K27me3 accumulation at telomeres and large pericentromeric interstitial telomeric repeat (ITR) domains by restricting DNA accessibility to Telomere Repeat Binding (TRB) proteins, a group of H1-related Myb factors mediating PRC2 cis recruitment. This study provides a mechanistic framework by which H1 avoids the formation of gigantic H3K27me3-rich domains at telomeric sequences and contributes to safeguard nucleus architecture.

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Cell Rep. 2023 Aug 29 ;42(8):112894. doi : 10.1016/j.celrep.2023.112894

Alternative splicing induced by bacterial pore-forming toxins sharpens CIRBP-mediated cell response to Listeria infection

Frédérique Godfroid — 2023-11-09T08:54:53Z

Authors :
Corre Morgane, Böhm Volker, Besic Vinko, Kurowska Anna, Viry Anouk, Mohammad Ammara, Sénamaud-Beaufort Catherine, Thomas-Chollier Morgane, Lebreton Alice

Abstract

Cell autonomous responses to intracellular bacteria largely depend on reorganization of gene expression. To gain isoform-level resolution of these modes of regulation, we combined long- and short-read transcriptomic analyses of the response of intestinal epithelial cells to infection by the foodborne pathogen Listeria monocytogenes. Among the most striking isoform-based types of regulation, expression of the cellular stress response regulator CIRBP (cold-inducible RNA-binding protein) and of several SRSFs (serine/arginine-rich splicing factors) switched from canonical transcripts to nonsense-mediated decay-sensitive isoforms by inclusion of ‘poison exons'. We showed that damage to host cell membranes caused by bacterial pore-forming toxins (listeriolysin O, perfringolysin, streptolysin or aerolysin) led to the dephosphorylation of SRSFs via the inhibition of the kinase activity of CLK1, thereby driving CIRBP alternative splicing. CIRBP isoform usage was found to have consequences on infection, since selective repression of canonical CIRBP reduced intracellular bacterial load while that of the poison exon-containing isoform exacerbated it. Consistently, CIRBP-bound mRNAs were shifted towards stress-relevant transcripts in infected cells, with increased mRNA levels or reduced translation efficiency for some targets. Our results thus generalize the alternative splicing of CIRBP and SRSFs as a common response to biotic or abiotic stresses by extending its relevance to the context of bacterial infection.

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Nucleic Acids Research. 2023 Nov 6 ; gkad1033 ; doi:10.1093/nar/gkad1033

Radial astrocyte synchronization modulates the visual system during behavioral-state transitions

Frédérique Godfroid — 2023-10-20T13:32:21Z

Authors :
Alejandro Uribe-Arias¹, Rotem Rozenblat^2,3, Ehud Vinepinsky^1,3, Emiliano Marachlian^1,3, Anirudh Kulkarni¹, David Zada², Martin Privat¹, Diego Topsakalian¹, Sarah Charpy¹, Virginie Candat¹, Sarah Nourin¹, Lior Appelbaum², Germán Sumbre^1,4,5,*

¹ Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France.
² The Faculty of Life Sciences and The Multidisciplinary Brain Research Center. Bar-Ilan University, Ramat-Gan, Israel.

Abstract

Glial cells support the function of neurons. Recent evidence shows that astrocytes are also involved in brain computations. To explore whether and how their excitable nature affects brain computations and motor behaviors, we used two-photon Ca2+ imaging of zebrafish larvae expressing GCaMP in both neurons and Radial Astrocytes (RAs). We found that, in the optic tectum, RAs synchronize their Ca2+ transients immediately after the end of an escape behavior. Using optogenetics, ablations and a genetically encoded norepinephrine sensor we observed that RA synchronous Ca2+ events are mediated by the locus-coeruleus-norepinephrine circuit. RA synchronization did not induce direct excitation or inhibition of tectal neurons. Nevertheless, it modulated the direction selectivity and the long-distance functional correlations among neurons. This mechanism supports freezing behavior following a switch to an alerted state. These results show that LC-mediated neuro-glia interactions modulate the visual system during transitions between behavioral states.

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Neuron 2023 Oct 19 ; doi.org/10.1016/j.neuron.2023.09.022

Revealing invisible cell phenotypes with conditional generative modeling

Frédérique Godfroid — 2023-10-12T12:52:48Z

Authors
Alexis Lamiable, Tiphaine Champetier, Francesco Leonardi, Ethan Cohen, Peter Sommer, David Hardy, Nicolas Argy, Achille Massougbodji, Elaine Del Nery, Gilles Cottrell, Yong-Jun Kwon & Auguste Genovesio

Abstract

Biological sciences, drug discovery and medicine rely heavily on cell phenotype perturbation and microscope observation. However, most cellular phenotypic changes are subtle and thus hidden from us by natural cell variability : two cells in the same condition already look different. In this study, we show that conditional generative models can be used to transform an image of cells from any one condition to another, thus canceling cell variability. We visually and quantitatively validate that the principle of synthetic cell perturbation works on discernible cases. We then illustrate its effectiveness in displaying otherwise invisible cell phenotypes triggered by blood cells under parasite infection, or by the presence of a disease-causing pathological mutation in differentiated neurons derived from iPSCs, or by low concentration drug treatments. The proposed approach, easy to use and robust, opens the door to more accessible discovery of biological and disease biomarkers.

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Nat Commun. 2023 Oct 11 ;14(1):6386. doi : 10.1038/s41467-023-42124-6

Deep Learning from Phylogenies for Diversification Analyses.

Frédérique Godfroid — 2023-09-29T08:02:20Z

Abstract

Birth-death models are widely used in combination with species phylogenies to study past diversification dynamics. Current inference approaches typically rely on likelihood-based methods. These methods are not generalizable, as a new likelihood formula must be established each time a new model is proposed ; for some models such formula is not even tractable. Deep learning can bring solutions in such situations, as deep neural networks can be trained to learn the relation between simulations and parameter values as a regression problem. In this paper, we adapt a recently developed deep learning method from pathogen phylodynamics to the case of diversification inference, and we extend its applicability to the case of the inference of state-dependent diversification models from phylogenies associated with trait data. We demonstrate the accuracy and time efficiency of the approach for the time constant homogeneous birth-death model and the Binary-State Speciation and Extinction model. Finally, we illustrate the use of the proposed inference machinery by reanalyzing a phylogeny of primates and their associated ecological role as seed dispersers. Deep learning inference provides at least the same accuracy as likelihood-based inference while being faster by several orders of magnitude, offering a promising new inference approach for deployment of future models in the field.

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Syst Biol. 2023 Aug 9 ; syad044. doi:10.1093/sysbio/syad044

Plasticity of thalamocortical axons is regulated by serotonin levels modulated by preterm birth

Frédérique Godfroid — 2023-09-06T13:28:56Z

Abstract

Sensory inputs are conveyed to distinct primary areas of the neocortex through specific thalamocortical axons (TCA). While TCA have the ability to reorient postnatally to rescue embryonic mistargeting and target proper modality-specific areas, how this remarkable adaptive process is regulated remains largely unknown. Here, using a mutant mouse model with a shifted TCA trajectory during embryogenesis, we demonstrated that TCA rewiring occurs during a short postnatal time window, preceded by a prenatal apoptosis of thalamic neurons-two processes that together lead to the formation of properly innervated albeit reduced primary sensory areas. We furthermore showed that preterm birth, through serotonin modulation, impairs early postnatal TCA plasticity, as well as the subsequent delineation of cortical area boundary. Our study defines a birth and serotonin-sensitive period that enables concerted adaptations of TCA to primary cortical areas with major implications for our understanding of brain wiring in physiological and preterm conditions.

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Proc Natl Acad Sci USA. 2023 Aug 15 ; 120(33):e2301644120. doi:10.1073/pnas.2301644120