1
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Colboc H, Moguelet P, Bazin D, Letavernier E, Sun C, Chessel A, Carvalho P, Lok C, Dillies AS, Chaby G, Maillard H, Kottler D, Goujon E, Jurus C, Panaye M, Tang E, Courville P, Boury A, Monfort JB, Chasset F, Senet P, Schanne-Klein MC. Elastic fiber alterations and calcifications in calcific uremic arteriolopathy. Sci Rep 2023; 13:15519. [PMID: 37726292 PMCID: PMC10509184 DOI: 10.1038/s41598-023-42492-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 09/11/2023] [Indexed: 09/21/2023] Open
Abstract
Calcific uremic arteriolopathy (CUA) is a severely morbid disease, affecting mostly dialyzed end-stage renal disease (ESRD) patients, associated with calcium deposits in the skin. Calcifications have been identified in ESRD patients without CUA, indicating that their presence is not specific to the disease. The objective of this retrospective multicenter study was to compare elastic fiber structure and skin calcifications in ESRD patients with CUA to those without CUA using innovative structural techniques. Fourteen ESRD patients with CUA were compared to 12 ESRD patients without CUA. Analyses of elastic fiber structure and skin calcifications using multiphoton microscopy followed by machine-learning analysis and field-emission scanning electron microscopy coupled with energy dispersive X-ray were performed. Elastic fibers specifically appeared fragmented in CUA. Quantitative analyses of multiphoton images showed that they were significantly straighter in ESRD patients with CUA than without CUA. Interstitial and vascular calcifications were observed in both groups of ESRD patients, but vascular calcifications specifically appeared massive and circumferential in CUA. Unlike interstitial calcifications, massive circumferential vascular calcifications and elastic fibers straightening appeared specific to CUA. The origins of such specific elastic fiber's alteration are still to be explored and may involve relationships with ischemic vascular or inflammatory processes.
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Affiliation(s)
- Hester Colboc
- Sorbonne Université, Hôpital Rothschild, Service Plaies et Cicatrisation, UMRS_1155, 5, Rue Santerre, 75012, Paris, France.
| | - Philippe Moguelet
- Sorbonne Université, Hôpital Tenon, Anatomie et Cytologie Pathologiques, Paris, France
| | - Dominique Bazin
- Université Paris-Saclay, CNRS, Institut de Chimie Physique, 91405, Orsay, France
| | - Emmanuel Letavernier
- Sorbonne Université, Hôpital Tenon, Service des Explorations Fonctionnelles Multidisciplinaires, UMRS_1155, Paris, France
| | - Chenyu Sun
- Laboratoire d'Optique et Biosciences, CNRS, Inserm, Ecole Polytechnique, Institut Polytechnique de Paris, Palaiseau, France
| | - Anatole Chessel
- Laboratoire d'Optique et Biosciences, CNRS, Inserm, Ecole Polytechnique, Institut Polytechnique de Paris, Palaiseau, France
| | - Priscille Carvalho
- Centre Hospitalier Universitaire de Rouen, Service de Dermatologie, Rouen, France
| | - Catherine Lok
- Centre Hospitalier Universitaire d'Amiens, Service de Dermatologie, Amiens, France
| | | | - Guillaume Chaby
- Centre Hospitalier Universitaire d'Amiens, Service de Dermatologie, Amiens, France
| | - Hervé Maillard
- Centre Hospitalier du Mans, Service de Dermatologie, Le Mans, France
| | - Diane Kottler
- Centre Hospitalier Universitaire de Caen, Service de Dermatologie, Caen, France
| | - Elisa Goujon
- Centre Hospitalier de Chalon-sur-Saône, Service de Dermatologie, Chalon, France
| | - Christine Jurus
- Clinique du Tonkin, Service de Médecine Vasculaire, Villeurbanne, France
| | - Marine Panaye
- Clinique du Tonkin, Service de Médecine Vasculaire, Villeurbanne, France
| | - Ellie Tang
- Sorbonne Université, Hôpital Tenon, Service des Explorations Fonctionnelles Multidisciplinaires, UMRS_1155, Paris, France
| | - Philippe Courville
- Centre Hospitalier Universitaire de Rouen, Anatomie et Cytologie Pathologiques, Rouen, France
| | - Antoine Boury
- Université Paris-Saclay, CNRS, Institut de Chimie Physique, 91405, Orsay, France
| | - Jean-Benoit Monfort
- Sorbonne Université, Faculté de Médecine, Service de Dermatologie et Allergologie, Hôpital Tenon, Paris, France
| | - François Chasset
- Sorbonne Université, Faculté de Médecine, Service de Dermatologie 3t Allergologie, Hôpital Tenon, INSERM U1135, CIMI, Paris, France
| | - Patricia Senet
- Sorbonne Université, Faculté de Médecine, Service de Dermatologie et Allergologie, Hôpital Tenon, Paris, France
| | - Marie-Claire Schanne-Klein
- Laboratoire d'Optique et Biosciences, CNRS, Inserm, Ecole Polytechnique, Institut Polytechnique de Paris, Palaiseau, France
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2
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Raoux C, Chessel A, Mahou P, Latour G, Schanne-Klein MC. Unveiling the lamellar structure of the human cornea over its full thickness using polarization-resolved SHG microscopy. Light Sci Appl 2023; 12:190. [PMID: 37528091 PMCID: PMC10394036 DOI: 10.1038/s41377-023-01224-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 06/22/2023] [Accepted: 07/05/2023] [Indexed: 08/03/2023]
Abstract
A key property of the human cornea is to maintain its curvature and consequently its refraction capability despite daily changes in intraocular pressure. This is closely related to the multiscale structure of the corneal stroma, which consists of 1-3 µm-thick stacked lamellae made of thin collagen fibrils. Nevertheless, the distribution, size, and orientation of these lamellae along the depth of the cornea are poorly characterized up to now. In this study, we use second harmonic generation (SHG) microscopy to visualize the collagen distribution over the full depth of 10 intact and unstained human corneas (500-600 µm thick). We take advantage of the small coherence length in epi-detection to axially resolve the lamellae while maintaining the corneal physiological curvature. Moreover, as raw epi-detected SHG images are spatially homogenous because of the sub-wavelength size of stromal collagen fibrils, we use a polarimetric approach to measure the collagen orientation in every voxel. After a careful validation of this approach, we show that the collagen lamellae (i) are mostly oriented along the inferior-superior axis in the anterior stroma and along the nasal-temporal axis in the posterior stroma, with a gradual shift in between and (ii) exhibit more disorder in the anterior stroma. These results represent the first quantitative characterization of the lamellar structure of the human cornea continuously along its entire thickness with micrometric resolution. It also shows the unique potential of P-SHG microscopy for imaging of collagen distribution in thick dense tissues.
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Affiliation(s)
- Clothilde Raoux
- Laboratory for Optics and Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128, Palaiseau, France
| | - Anatole Chessel
- Laboratory for Optics and Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128, Palaiseau, France
| | - Pierre Mahou
- Laboratory for Optics and Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128, Palaiseau, France
| | - Gaël Latour
- Laboratory for Optics and Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128, Palaiseau, France
- Université Paris-Saclay, 91190, Gif-sur-Yvette, France
| | - Marie-Claire Schanne-Klein
- Laboratory for Optics and Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128, Palaiseau, France.
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3
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Phan MS, Matho K, Beaurepaire E, Livet J, Chessel A. nAdder: A scale-space approach for the 3D analysis of neuronal traces. PLoS Comput Biol 2022; 18:e1010211. [PMID: 35789212 PMCID: PMC9286273 DOI: 10.1371/journal.pcbi.1010211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 07/15/2022] [Accepted: 05/16/2022] [Indexed: 11/19/2022] Open
Abstract
Tridimensional microscopy and algorithms for automated segmentation and tracing are revolutionizing neuroscience through the generation of growing libraries of neuron reconstructions. Innovative computational methods are needed to analyze these neuronal traces. In particular, means to characterize the geometric properties of traced neurites along their trajectory have been lacking. Here, we propose a local tridimensional (3D) scale metric derived from differential geometry, measuring for each point of a curve the characteristic length where it is fully 3D as opposed to being embedded in a 2D plane or 1D line. The larger this metric is and the more complex the local 3D loops and turns of the curve are. Available through the GeNePy3D open-source Python quantitative geometry library (https://genepy3d.gitlab.io), this approach termed nAdder offers new means of describing and comparing axonal and dendritic arbors. We validate this metric on simulated and real traces. By reanalysing a published zebrafish larva whole brain dataset, we show its ability to characterize different population of commissural axons, distinguish afferent connections to a target region and differentiate portions of axons and dendrites according to their behavior, shedding new light on the stereotypical nature of neurites' local geometry.
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Affiliation(s)
- Minh Son Phan
- Laboratory for Optics and Biosciences, CNRS, INSERM, Ecole Polytechnique, IP Paris, Palaiseau, France
- Institut Pasteur, Université de Paris Cité, Image Analysis Hub,Paris, France
| | - Katherine Matho
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Emmanuel Beaurepaire
- Laboratory for Optics and Biosciences, CNRS, INSERM, Ecole Polytechnique, IP Paris, Palaiseau, France
| | - Jean Livet
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Anatole Chessel
- Laboratory for Optics and Biosciences, CNRS, INSERM, Ecole Polytechnique, IP Paris, Palaiseau, France
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4
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Ung TPL, Lim S, Solinas X, Mahou P, Chessel A, Marionnet C, Bornschlögl T, Beaurepaire E, Bernerd F, Pena AM, Stringari C. Simultaneous NAD(P)H and FAD fluorescence lifetime microscopy of long UVA-induced metabolic stress in reconstructed human skin. Sci Rep 2021; 11:22171. [PMID: 34772978 PMCID: PMC8589997 DOI: 10.1038/s41598-021-00126-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 10/07/2021] [Indexed: 11/17/2022] Open
Abstract
Solar ultraviolet longwave UVA1 exposure of human skin has short-term consequences at cellular and molecular level, leading at long-term to photoaging. Following exposure, reactive oxygen species (ROS) are generated, inducing oxidative stress that might impair cellular metabolic activity. However, the dynamic of UVA1 impact on cellular metabolism remains unknown because of lacking adequate live imaging techniques. Here we assess the UVA1-induced metabolic stress response in reconstructed human skin with multicolor two-photon fluorescence lifetime microscopy (FLIM). Simultaneous imaging of nicotinamide adenine dinucleotide (NAD(P)H) and flavin adenine dinucleotide (FAD) by wavelength mixing allows quantifying cellular metabolism in function of NAD(P)+/NAD(P)H and FAD/FADH2 redox ratios. After UVA1 exposure, we observe an increase of fraction of bound NAD(P)H and decrease of fraction of bound FAD indicating a metabolic switch from glycolysis to oxidative phosphorylation or oxidative stress possibly correlated to ROS generation. NAD(P)H and FAD biomarkers have unique temporal dynamic and sensitivity to skin cell types and UVA1 dose. While the FAD biomarker is UVA1 dose-dependent in keratinocytes, the NAD(P)H biomarker shows no dose dependence in keratinocytes, but is directly affected after exposure in fibroblasts, thus reflecting different skin cells sensitivities to oxidative stress. Finally, we show that a sunscreen including a UVA1 filter prevents UVA1 metabolic stress response from occurring.
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Affiliation(s)
- Thi Phuong Lien Ung
- Laboratory for Optics and Biosciences, Ecole polytechnique, CNRS, INSERM, IP Paris, 91128, Palaiseau Cedex, France
| | - Seongbin Lim
- Laboratory for Optics and Biosciences, Ecole polytechnique, CNRS, INSERM, IP Paris, 91128, Palaiseau Cedex, France
| | - Xavier Solinas
- Laboratory for Optics and Biosciences, Ecole polytechnique, CNRS, INSERM, IP Paris, 91128, Palaiseau Cedex, France
| | - Pierre Mahou
- Laboratory for Optics and Biosciences, Ecole polytechnique, CNRS, INSERM, IP Paris, 91128, Palaiseau Cedex, France
| | - Anatole Chessel
- Laboratory for Optics and Biosciences, Ecole polytechnique, CNRS, INSERM, IP Paris, 91128, Palaiseau Cedex, France
| | - Claire Marionnet
- L'Oréal Research and Innovation, 1 avenue Eugène Schueller BP 22, 93601, Aulnay-sous-Bois, France
| | - Thomas Bornschlögl
- L'Oréal Research and Innovation, 1 avenue Eugène Schueller BP 22, 93601, Aulnay-sous-Bois, France
| | - Emmanuel Beaurepaire
- Laboratory for Optics and Biosciences, Ecole polytechnique, CNRS, INSERM, IP Paris, 91128, Palaiseau Cedex, France
| | - Françoise Bernerd
- L'Oréal Research and Innovation, 1 avenue Eugène Schueller BP 22, 93601, Aulnay-sous-Bois, France
| | - Ana-Maria Pena
- L'Oréal Research and Innovation, 1 avenue Eugène Schueller BP 22, 93601, Aulnay-sous-Bois, France.
| | - Chiara Stringari
- Laboratory for Optics and Biosciences, Ecole polytechnique, CNRS, INSERM, IP Paris, 91128, Palaiseau Cedex, France.
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5
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Abstract
The advent of large-scale fluorescence and electronic microscopy techniques along with maturing image analysis is giving life sciences a deluge of geometrical objects in 2D/3D(+t) to deal with. These objects take the form of large scale, localised, precise, single cell, quantitative data such as cells' positions, shapes, trajectories or lineages, axon traces in whole brains atlases or varied intracellular protein localisations, often in multiple experimental conditions. The data mining of those geometrical objects requires a variety of mathematical and computational tools of diverse accessibility and complexity. Here we present a new Python library for quantitative 3D geometry called GeNePy3D which helps handle and mine information and knowledge from geometric data, providing a unified application programming interface (API) to methods from several domains including computational geometry, scale space methods or spatial statistics. By framing this library as generically as possible, and by linking it to as many state-of-the-art reference algorithms and projects as needed, we help render those often specialist methods accessible to a larger community. We exemplify the usefulness of the GeNePy3D toolbox by re-analysing a recently published whole-brain zebrafish neuronal atlas, with other applications and examples available online. Along with an open source, documented and exemplified code, we release reusable containers to allow for convenient and wide usability and increased reproducibility.
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Affiliation(s)
- Minh-Son Phan
- Laboratory of Optics and Biosciences, CNRS, INSERM, Ecole polytechniqe, Institut polytechnique de Paris, Palaiseau, 91120, France
| | - Anatole Chessel
- Laboratory of Optics and Biosciences, CNRS, INSERM, Ecole polytechniqe, Institut polytechnique de Paris, Palaiseau, 91120, France
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6
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Phan MS, Chessel A. GeNePy3D: a quantitative geometry python toolbox for bioimaging. F1000Res 2020; 9:1374. [PMID: 34249350 PMCID: PMC8226399 DOI: 10.12688/f1000research.27395.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/14/2021] [Indexed: 11/20/2022] Open
Abstract
The advent of large-scale fluorescence and electronic microscopy techniques along with maturing image analysis is giving life sciences a deluge of geometrical objects in 2D/3D(+t) to deal with. These objects take the form of large scale, localised, precise, single cell, quantitative data such as cells' positions, shapes, trajectories or lineages, axon traces in whole brains atlases or varied intracellular protein localisations, often in multiple experimental conditions. The data mining of those geometrical objects requires a variety of mathematical and computational tools of diverse accessibility and complexity. Here we present a new Python library for quantitative 3D geometry called GeNePy3D which helps handle and mine information and knowledge from geometric data, providing a unified application programming interface (API) to methods from several domains including computational geometry, scale space methods or spatial statistics. By framing this library as generically as possible, and by linking it to as many state-of-the-art reference algorithms and projects as needed, we help render those often specialist methods accessible to a larger community. We exemplify the usefulness of the GeNePy3D toolbox by re-analysing a recently published whole-brain zebrafish neuronal atlas, with other applications and examples available online. Along with an open source, documented and exemplified code, we release reusable containers to allow for convenient and wide usability and increased reproducibility.
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Affiliation(s)
- Minh-Son Phan
- Laboratory of Optics and Biosciences, CNRS, INSERM, Ecole polytechniqe, Institut polytechnique de Paris, Palaiseau, 91120, France
| | - Anatole Chessel
- Laboratory of Optics and Biosciences, CNRS, INSERM, Ecole polytechniqe, Institut polytechnique de Paris, Palaiseau, 91120, France
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7
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Chessel A, Carazo Salas RE. From observing to predicting single-cell structure and function with high-throughput/high-content microscopy. Essays Biochem 2019; 63:197-208. [PMID: 31243141 PMCID: PMC6610450 DOI: 10.1042/ebc20180044] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 05/24/2019] [Accepted: 05/24/2019] [Indexed: 02/08/2023]
Abstract
In the past 15 years, cell-based microscopy has evolved its focus from observing cell function to aiming to predict it. In particular-powered by breakthroughs in computer vision, large-scale image analysis and machine learning-high-throughput and high-content microscopy imaging have enabled to uniquely harness single-cell information to systematically discover and annotate genes and regulatory pathways, uncover systems-level interactions and causal links between cellular processes, and begin to clarify and predict causal cellular behaviour and decision making. Here we review these developments, discuss emerging trends in the field, and describe how single-cell 'omics and single-cell microscopy are imminently in an intersecting trajectory. The marriage of these two fields will make possible an unprecedented understanding of cell and tissue behaviour and function.
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Affiliation(s)
- Anatole Chessel
- École polytechnique, Université Paris-Saclay, 91128 Palaiseau Cedex, France
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8
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Williams E, Moore J, Li SW, Rustici G, Tarkowska A, Chessel A, Leo S, Antal B, Ferguson RK, Sarkans U, Brazma A, Salas REC, Swedlow JR. The Image Data Resource: A Bioimage Data Integration and Publication Platform. Nat Methods 2017; 14:775-781. [PMID: 28775673 PMCID: PMC5536224 DOI: 10.1038/nmeth.4326] [Citation(s) in RCA: 141] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
This Resource describes the Image Data Resource (IDR), a prototype online system for biological image data that links experimental and analytic data across multiple data sets and promotes image data sharing and reanalysis. Access to primary research data is vital for the advancement of science. To extend the data types supported by community repositories, we built a prototype Image Data Resource (IDR). IDR links data from several imaging modalities, including high-content screening, multi-dimensional microscopy and digital pathology, with public genetic or chemical databases and cell and tissue phenotypes expressed using controlled ontologies. Using this integration, IDR facilitates the analysis of gene networks and reveals functional interactions that are inaccessible to individual studies. To enable reanalysis, we also established a computational resource based on Jupyter notebooks that allows remote access to the entire IDR. IDR is also an open-source platform for publishing imaging data. Thus IDR provides an online resource and a software infrastructure that promotes and extends publication and reanalysis of scientific image data.
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Affiliation(s)
- Eleanor Williams
- Centre for Gene Regulation & Expression & Division of Computational Biology, University of Dundee, Dundee, Scotland, UK.,European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom
| | - Josh Moore
- Centre for Gene Regulation & Expression & Division of Computational Biology, University of Dundee, Dundee, Scotland, UK
| | - Simon W Li
- Centre for Gene Regulation & Expression & Division of Computational Biology, University of Dundee, Dundee, Scotland, UK
| | - Gabriella Rustici
- Centre for Gene Regulation & Expression & Division of Computational Biology, University of Dundee, Dundee, Scotland, UK
| | - Aleksandra Tarkowska
- Centre for Gene Regulation & Expression & Division of Computational Biology, University of Dundee, Dundee, Scotland, UK
| | - Anatole Chessel
- Pharmacology & Genetics Departments and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK.,LOB, Ecole Polytechnique, CNRS, INSERM, Université Paris-Saclay, Palaiseau, France
| | - Simone Leo
- Centre for Gene Regulation & Expression & Division of Computational Biology, University of Dundee, Dundee, Scotland, UK.,Center for Advanced Studies, Research, and Development in Sardinia (CRS4), Pula(CA), Italy
| | - Bálint Antal
- Pharmacology & Genetics Departments and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
| | - Richard K Ferguson
- Centre for Gene Regulation & Expression & Division of Computational Biology, University of Dundee, Dundee, Scotland, UK
| | - Ugis Sarkans
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom
| | - Alvis Brazma
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom
| | - Rafael E Carazo Salas
- Pharmacology & Genetics Departments and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK.,School of Cell and Molecular Medicine, University of Bristol, Bristol, UK
| | - Jason R Swedlow
- Centre for Gene Regulation & Expression & Division of Computational Biology, University of Dundee, Dundee, Scotland, UK
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9
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Abstract
High-throughput/high-content microscopy-based screens are powerful tools for functional genomics, yielding intracellular information down to the level of single-cells for thousands of genotypic conditions. However, accessing their data requires specialized knowledge and most often that data is no longer analyzed after initial publication. We describe Mineotaur (http://www.mineotaur.org), a open-source, downloadable web application that allows easy online sharing and interactive visualisation of large screen datasets, facilitating their dissemination and further analysis, and enhancing their impact.
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Affiliation(s)
- Bálint Antal
- Genetics Department, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK.
| | - Anatole Chessel
- Genetics Department, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK.
| | - Rafael E Carazo Salas
- Genetics Department, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK.
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10
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Abenza JF, Couturier E, Dodgson J, Dickmann J, Chessel A, Dumais J, Salas REC. Wall mechanics and exocytosis define the shape of growth domains in fission yeast. Nat Commun 2015; 6:8400. [PMID: 26455310 PMCID: PMC4618311 DOI: 10.1038/ncomms9400] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 08/19/2015] [Indexed: 11/14/2022] Open
Abstract
The amazing structural variety of cells is matched only by their functional diversity, and reflects the complex interplay between biochemical and mechanical regulation. How both regulatory layers generate specifically shaped cellular domains is not fully understood. Here, we report how cell growth domains are shaped in fission yeast. Based on quantitative analysis of cell wall expansion and elasticity, we develop a model for how mechanics and cell wall assembly interact and use it to look for factors underpinning growth domain morphogenesis. Surprisingly, we find that neither the global cell shape regulators Cdc42-Scd1-Scd2 nor the major cell wall synthesis regulators Bgs1-Bgs4-Rgf1 are reliable predictors of growth domain geometry. Instead, their geometry can be defined by cell wall mechanics and the cortical localization pattern of the exocytic factors Sec6-Syb1-Exo70. Forceful re-directioning of exocytic vesicle fusion to broader cortical areas induces proportional shape changes to growth domains, demonstrating that both features are causally linked. Cell shape is determined by a combination of biochemical regulation and mechanical forces. By imaging the dynamic behaviour of growth regulatory proteins in fission yeast and integrating these data within a mechanical model, Abenza et al. find that exocytosis plays a dominant role in shaping growth domains.
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Affiliation(s)
- Juan F Abenza
- Genetics Department, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK.,Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
| | - Etienne Couturier
- Departamento de Física, Universidad de Santiago de Chile, Santiago, Chile
| | - James Dodgson
- Genetics Department, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK.,Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
| | - Johanna Dickmann
- Genetics Department, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK.,Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
| | - Anatole Chessel
- Genetics Department, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK.,Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
| | - Jacques Dumais
- Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez, Viña del Mar 2562307, Chile.,Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, Massachusetts 02138, USA
| | - Rafael E Carazo Salas
- Genetics Department, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK.,Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
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11
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Jeffares DC, Rallis C, Rieux A, Speed D, Převorovský M, Mourier T, Marsellach FX, Iqbal Z, Lau W, Cheng TM, Pracana R, Mülleder M, Lawson JL, Chessel A, Bala S, Hellenthal G, O’Fallon B, Keane T, Simpson JT, Bischof L, Tomiczek B, Bitton DA, Sideri T, Codlin S, Hellberg JE, van Trigt L, Jeffery L, Li JJ, Atkinson S, Thodberg M, Febrer M, McLay K, Drou N, Brown W, Hayles J, Carazo Salas RE, Ralser M, Maniatis N, Balding DJ, Balloux F, Durbin R, Bähler J. The genomic and phenotypic diversity of Schizosaccharomyces pombe. Nat Genet 2015; 47:235-41. [PMID: 25665008 PMCID: PMC4645456 DOI: 10.1038/ng.3215] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 01/14/2015] [Indexed: 12/14/2022]
Abstract
Natural variation within species reveals aspects of genome evolution and function. The fission yeast Schizosaccharomyces pombe is an important model for eukaryotic biology, but researchers typically use one standard laboratory strain. To extend the usefulness of this model, we surveyed the genomic and phenotypic variation in 161 natural isolates. We sequenced the genomes of all strains, finding moderate genetic diversity (π = 3 × 10(-3) substitutions/site) and weak global population structure. We estimate that dispersal of S. pombe began during human antiquity (∼340 BCE), and ancestors of these strains reached the Americas at ∼1623 CE. We quantified 74 traits, finding substantial heritable phenotypic diversity. We conducted 223 genome-wide association studies, with 89 traits showing at least one association. The most significant variant for each trait explained 22% of the phenotypic variance on average, with indels having larger effects than SNPs. This analysis represents a rich resource to examine genotype-phenotype relationships in a tractable model.
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Affiliation(s)
- Daniel C. Jeffares
- Department of Genetics, Evolution & Environment, University College London, London, UK
| | - Charalampos Rallis
- Department of Genetics, Evolution & Environment, University College London, London, UK
| | - Adrien Rieux
- Department of Genetics, Evolution & Environment, University College London, London, UK
- UCL Genetics Institute, University College London, London, UK
| | - Doug Speed
- Department of Genetics, Evolution & Environment, University College London, London, UK
- UCL Genetics Institute, University College London, London, UK
| | - Martin Převorovský
- Department of Cell Biology, Charles University in Prague, Prague, Czech Republic
| | - Tobias Mourier
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | | | - Zamin Iqbal
- Wellcome Trust Centre for Human Genetics, Oxford, UK
| | - Winston Lau
- Department of Genetics, Evolution & Environment, University College London, London, UK
| | - Tammy M.K. Cheng
- Cell Cycle Laboratory, Cancer Research UK London Research Institute, London, UK
| | - Rodrigo Pracana
- Department of Genetics, Evolution & Environment, University College London, London, UK
| | - Michael Mülleder
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Jonathan L.D. Lawson
- Department of Genetics, University of Cambridge, Cambridge, UK
- The Gurdon Institute, University of Cambridge, Cambridge, UK
| | - Anatole Chessel
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Sendu Bala
- Wellcome Trust Sanger Institute, Cambridge, UK
| | - Garrett Hellenthal
- Department of Genetics, Evolution & Environment, University College London, London, UK
- UCL Genetics Institute, University College London, London, UK
| | | | | | | | - Leanne Bischof
- CSIRO Mathematics, Informatics and Statistics, North Ryde, Australia; The Genome Analysis Centre, Norwich, UK
| | - Bartlomiej Tomiczek
- Department of Genetics, Evolution & Environment, University College London, London, UK
| | - Danny A. Bitton
- Department of Genetics, Evolution & Environment, University College London, London, UK
| | - Theodora Sideri
- Department of Genetics, Evolution & Environment, University College London, London, UK
| | - Sandra Codlin
- Department of Genetics, Evolution & Environment, University College London, London, UK
| | | | - Laurent van Trigt
- Department of Genetics, Evolution & Environment, University College London, London, UK
| | - Linda Jeffery
- Cell Cycle Laboratory, Cancer Research UK London Research Institute, London, UK
| | - Juan-Juan Li
- Cell Cycle Laboratory, Cancer Research UK London Research Institute, London, UK
| | - Sophie Atkinson
- Department of Genetics, Evolution & Environment, University College London, London, UK
| | - Malte Thodberg
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Melanie Febrer
- CSIRO Mathematics, Informatics and Statistics, North Ryde, Australia; The Genome Analysis Centre, Norwich, UK
| | - Kirsten McLay
- CSIRO Mathematics, Informatics and Statistics, North Ryde, Australia; The Genome Analysis Centre, Norwich, UK
| | - Nizar Drou
- CSIRO Mathematics, Informatics and Statistics, North Ryde, Australia; The Genome Analysis Centre, Norwich, UK
| | - William Brown
- Centre for Genetics and Genomics, The University of Nottingham, Nottingham, UK
| | - Jacqueline Hayles
- Cell Cycle Laboratory, Cancer Research UK London Research Institute, London, UK
| | - Rafael E. Carazo Salas
- Department of Genetics, University of Cambridge, Cambridge, UK
- The Gurdon Institute, University of Cambridge, Cambridge, UK
| | - Markus Ralser
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
- Division of Physiology and Metabolism, MRC National Institute for Medical Research, London, UK
| | - Nikolas Maniatis
- Department of Genetics, Evolution & Environment, University College London, London, UK
| | - David J. Balding
- Department of Genetics, Evolution & Environment, University College London, London, UK
- UCL Genetics Institute, University College London, London, UK
| | - Francois Balloux
- Department of Genetics, Evolution & Environment, University College London, London, UK
- UCL Genetics Institute, University College London, London, UK
| | | | - Jürg Bähler
- Department of Genetics, Evolution & Environment, University College London, London, UK
- UCL Genetics Institute, University College London, London, UK
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12
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Pécot T, Bouthemy P, Boulanger J, Chessel A, Bardin S, Salamero J, Kervrann C. Background fluorescence estimation and vesicle segmentation in live cell imaging with conditional random fields. IEEE Trans Image Process 2015; 24:667-80. [PMID: 25531952 DOI: 10.1109/tip.2014.2380178] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Image analysis applied to fluorescence live cell microscopy has become a key tool in molecular biology since it enables to characterize biological processes in space and time at the subcellular level. In fluorescence microscopy imaging, the moving tagged structures of interest, such as vesicles, appear as bright spots over a static or nonstatic background. In this paper, we consider the problem of vesicle segmentation and time-varying background estimation at the cellular scale. The main idea is to formulate the joint segmentation-estimation problem in the general conditional random field framework. Furthermore, segmentation of vesicles and background estimation are alternatively performed by energy minimization using a min cut-max flow algorithm. The proposed approach relies on a detection measure computed from intensity contrasts between neighboring blocks in fluorescence microscopy images. This approach permits analysis of either 2D + time or 3D + time data. We demonstrate the performance of the so-called C-CRAFT through an experimental comparison with the state-of-the-art methods in fluorescence video-microscopy. We also use this method to characterize the spatial and temporal distribution of Rab6 transport carriers at the cell periphery for two different specific adhesion geometries.
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13
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Graml V, Studera X, Lawson JLD, Chessel A, Geymonat M, Bortfeld-Miller M, Walter T, Wagstaff L, Piddini E, Carazo Salas RE. A genomic Multiprocess survey of machineries that control and link cell shape, microtubule organization, and cell-cycle progression. Dev Cell 2015; 31:227-239. [PMID: 25373780 DOI: 10.1016/j.devcel.2014.09.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2013] [Revised: 04/21/2014] [Accepted: 08/19/2014] [Indexed: 12/17/2022]
Abstract
Understanding cells as integrated systems requires that we systematically decipher how single genes affect multiple biological processes and how processes are functionally linked. Here, we used multiprocess phenotypic profiling, combining high-resolution 3D confocal microscopy and multiparametric image analysis, to simultaneously survey the fission yeast genome with respect to three key cellular processes: cell shape, microtubule organization, and cell-cycle progression. We identify, validate, and functionally annotate 262 genes controlling specific aspects of those processes. Of these, 62% had not been linked to these processes before and 35% are implicated in multiple processes. Importantly, we identify a conserved role for DNA-damage responses in controlling microtubule stability. In addition, we investigate how the processes are functionally linked. We show unexpectedly that disruption of cell-cycle progression does not necessarily affect cell size control and that distinct aspects of cell shape regulate microtubules and vice versa, identifying important systems-level links across these processes.
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Affiliation(s)
- Veronika Graml
- The Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, United Kingdom.,Genetics Department, University of Cambridge, Downing Street, Cambridge, CB2 3EH, United Kingdom.,Institute of Biochemistry, ETH Zurich, Schafmattstrasse 18, HPM G16.2, Zurich, CH-8093, Switzerland
| | - Xenia Studera
- The Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, United Kingdom.,Genetics Department, University of Cambridge, Downing Street, Cambridge, CB2 3EH, United Kingdom.,Institute of Biochemistry, ETH Zurich, Schafmattstrasse 18, HPM G16.2, Zurich, CH-8093, Switzerland
| | - Jonathan L D Lawson
- The Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, United Kingdom.,Genetics Department, University of Cambridge, Downing Street, Cambridge, CB2 3EH, United Kingdom
| | - Anatole Chessel
- The Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, United Kingdom.,Genetics Department, University of Cambridge, Downing Street, Cambridge, CB2 3EH, United Kingdom
| | - Marco Geymonat
- The Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, United Kingdom.,Genetics Department, University of Cambridge, Downing Street, Cambridge, CB2 3EH, United Kingdom
| | - Miriam Bortfeld-Miller
- Institute of Biochemistry, ETH Zurich, Schafmattstrasse 18, HPM G16.2, Zurich, CH-8093, Switzerland
| | - Thomas Walter
- Institut Curie, Centre for Computational Biology, Centre de Recherche Unité 900, 26 Rue d'Ulm, 75248 Paris, France
| | - Laura Wagstaff
- The Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, United Kingdom.,Zoology Department, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, United Kingdom
| | - Eugenia Piddini
- The Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, United Kingdom.,Zoology Department, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, United Kingdom
| | - Rafael E Carazo Salas
- The Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, United Kingdom.,Genetics Department, University of Cambridge, Downing Street, Cambridge, CB2 3EH, United Kingdom.,Institute of Biochemistry, ETH Zurich, Schafmattstrasse 18, HPM G16.2, Zurich, CH-8093, Switzerland
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14
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Dodgson J, Chessel A, Cox S, Carazo Salas RE. Super-Resolution Microscopy: SIM, STED and Localization Microscopy. Fungal Biol 2015. [DOI: 10.1007/978-3-319-22437-4_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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15
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Abstract
Every cell has a characteristic shape key to its fate and function. That shape is not only the product of genetic design and of the physical and biochemical environment, but it is also subject to inheritance. However, the nature and contribution of cell shape inheritance to morphogenetic control is mostly ignored. Here, we investigate morphogenetic inheritance in the cylindrically-shaped fission yeast Schizosaccharomyces pombe. Focusing on sixteen different ‘curved’ mutants - a class of mutants which often fail to grow axially straight – we quantitatively characterize their dynamics of cell shape inheritance throughout generations. We show that mutants of similar machineries display similar dynamics of cell shape inheritance, and exploit this feature to show that persistent axial cell growth in S. pombe is secured by multiple, separable molecular pathways. Finally, we find that one of those pathways corresponds to the swc2-swr1-vps71 SWR1/SRCAP chromatin remodelling complex, which acts additively to the known mal3-tip1-mto1-mto2 microtubule and tea1-tea2-tea4-pom1 polarity machineries.
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Affiliation(s)
- Juan F. Abenza
- The Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
- * E-mail: (JFA); (REC-S)
| | - Anatole Chessel
- The Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
| | - William G. Raynaud
- The Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
| | - Rafael E. Carazo-Salas
- The Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
- * E-mail: (JFA); (REC-S)
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16
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Vaggi F, Schiavinotto T, Lawson JL, Chessel A, Dodgson J, Geymonat M, Sato M, Carazo Salas RE, Csikász-Nagy A. A network approach to mixing delegates at meetings. eLife 2014; 3:e02273. [PMID: 24497549 PMCID: PMC3912938 DOI: 10.7554/elife.02273] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Delegates at scientific meetings can come from diverse backgrounds and use very different methods in their research. Promoting interactions between these ‘distant’ delegates is challenging but such interactions could lead to novel interdisciplinary collaborations and unexpected breakthroughs. We have developed a network-based ‘speed dating’ approach that allows us to initiate such distant interactions by pairing every delegate with another delegate who might be of interest to them, but whom they might never have encountered otherwise. Here we describe our approach and its algorithmic implementation.
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Affiliation(s)
- Federico Vaggi
- Federico Vaggi is in the Department of Computational Biology, Fondazione Edmund Mach, San Michele all'Adige, Italy
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17
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Dodgson J, Chessel A, Yamamoto M, Vaggi F, Cox S, Rosten E, Albrecht D, Geymonat M, Csikasz-Nagy A, Sato M, Carazo-Salas RE. Spatial segregation of polarity factors into distinct cortical clusters is required for cell polarity control. Nat Commun 2013; 4:1834. [PMID: 23673619 PMCID: PMC3674234 DOI: 10.1038/ncomms2813] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Accepted: 03/26/2013] [Indexed: 01/06/2023] Open
Abstract
Cell polarity is regulated by evolutionarily conserved polarity factors whose precise higher-order organization at the cell cortex is largely unknown. Here we image frontally the cortex of live fission yeast cells using time-lapse and super-resolution microscopy. Interestingly, we find that polarity factors are organized in discrete cortical clusters resolvable to ~50–100 nm in size, which can form and become cortically enriched by oligomerization. We show that forced co-localization of the polarity factors Tea1 and Tea3 results in polarity defects, suggesting that the maintenance of both factors in distinct clusters is required for polarity. However, during mitosis, their co-localization increases, and Tea3 helps to retain the cortical localization of the Tea1 growth landmark in preparation for growth reactivation following mitosis. Thus, regulated spatial segregation of polarity factor clusters provides a means to spatio-temporally control cell polarity at the cell cortex. We observe similar clusters in Saccharomyces cerevisiae and Caenorhabditis elegans cells, indicating this could be a universal regulatory feature. Cell polarity is generated and maintained by the spatial accumulation of polarity factors. By imaging fission yeast cells ‘end-on’, the authors show that the polarity factors Tea1 and Tea3 segregate into distinct clusters, and that surprisingly, their segregation is critical for cell polarization.
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Affiliation(s)
- James Dodgson
- The Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK
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18
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Lecourtier L, Deschaux O, Arnaud C, Chessel A, Kelly PH, Garcia R. Habenula lesions alter synaptic plasticity within the fimbria-accumbens pathway in the rat. Neuroscience 2006; 141:1025-1032. [PMID: 16716523 DOI: 10.1016/j.neuroscience.2006.04.018] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2005] [Revised: 04/07/2006] [Accepted: 04/14/2006] [Indexed: 10/24/2022]
Abstract
Both the habenula and the nucleus accumbens, and especially the glutamatergic innervation of the latter from the hippocampus, have been hypothesized to be involved, in different ways, in the pathophysiology of cognitive disturbances in schizophrenia. Lesions of the habenula produce disturbances of memory and attention in experimental animals. As the habenular nuclei have been shown to influence the release of many neurotransmitters, both in the hippocampus and the nucleus accumbens, we examined in this study the effects of bilateral habenula lesions on the plasticity of the fimbria-nucleus accumbens pathway, by means of the long-term depression phenomenon in freely moving rats. Long-term depression, induced within the shell region of the nucleus accumbens by low-frequency stimulation of the fimbria, was exaggerated and showed greater persistence in habenula-lesioned rats compared with sham-operated animals. These results indicate that plasticity in the fimbria-nucleus accumbens pathway is altered by habenula lesions in a way similar to previously-reported effects of stress and the psychosis-provoking agent ketamine. Moreover, they strengthen the views that the habenula belongs to systems, mediating higher cognitive functions, which involve the hippocampus and the nucleus accumbens. Finally, this study suggests that dysfunction of the habenula could contribute to cognitive alterations in diseases such as schizophrenia, where the habenula is reported to exhibit exaggerated calcification.
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Affiliation(s)
- L Lecourtier
- NS Research, Novartis Institutes for Biomedical Research, Basel, Switzerland.
| | - O Deschaux
- INSERM, Equipe Avenir, Laboratoire de Neurobiologie et Psychopathologie, Université de Nice Sophia-Antipolis, Nice, France
| | - C Arnaud
- INSERM, Equipe Avenir, Laboratoire de Neurobiologie et Psychopathologie, Université de Nice Sophia-Antipolis, Nice, France
| | - A Chessel
- INSERM, Equipe Avenir, Laboratoire de Neurobiologie et Psychopathologie, Université de Nice Sophia-Antipolis, Nice, France
| | - P H Kelly
- NS Research, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - R Garcia
- INSERM, Equipe Avenir, Laboratoire de Neurobiologie et Psychopathologie, Université de Nice Sophia-Antipolis, Nice, France
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