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Lazo OM, Schiavo G. Rab10 regulates the sorting of internalised TrkB for retrograde axonal transport. eLife 2023; 12:81532. [PMID: 36897066 PMCID: PMC10005780 DOI: 10.7554/elife.81532] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 02/15/2023] [Indexed: 03/11/2023] Open
Abstract
Neurons process real-time information from axon terminals to coordinate gene expression, growth, and plasticity. Inputs from distal axons are encoded as a stream of endocytic organelles, termed signalling endosomes, targeted to the soma. Formation of these organelles depends on target-derived molecules, such as brain-derived neurotrophic factor (BDNF), which is recognised by TrkB receptors on the plasma membrane, endocytosed, and transported to the cell body along the microtubules network. Notwithstanding its physiological and neuropathological importance, the mechanism controlling the sorting of TrkB to signalling endosomes is currently unknown. In this work, we use primary mouse neurons to uncover the small GTPase Rab10 as critical for TrkB sorting and propagation of BDNF signalling from axon terminals to the soma. Our data demonstrate that Rab10 defines a novel membrane compartment that is rapidly mobilised towards the axon terminal upon BDNF stimulation, enabling the axon to fine-tune retrograde signalling depending on BDNF availability at the synapse. These results help clarifying the neuroprotective phenotype recently associated to Rab10 polymorphisms in Alzheimer's disease and provide a new therapeutic target to halt neurodegeneration.
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Affiliation(s)
- Oscar Marcelo Lazo
- Department of Neuromuscular Diseases and UCL Queen Square Motor Neuron Disease Centre, UCL Queen Square Institute of Neurology, University College LondonLondonUnited Kingdom
- UK Dementia Research Institute at UCLLondonUnited Kingdom
| | - Giampietro Schiavo
- Department of Neuromuscular Diseases and UCL Queen Square Motor Neuron Disease Centre, UCL Queen Square Institute of Neurology, University College LondonLondonUnited Kingdom
- UK Dementia Research Institute at UCLLondonUnited Kingdom
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2
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Synaptotagmin 2 is ectopically overexpressed in excitatory presynapses of a widely used CaMKΙΙα-Cre mouse line. iScience 2022; 25:104692. [PMID: 35856033 PMCID: PMC9287804 DOI: 10.1016/j.isci.2022.104692] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 04/29/2022] [Accepted: 06/27/2022] [Indexed: 12/13/2022] Open
Abstract
The CaMKΙΙα-Cre mouse lines, possibly the most used Cre lines in neuroscience, have resulted in over 800 articles to date. Here, we demonstrate that the second most widely used CaMKΙΙα-Cre line, Tg(Camk2a-cre)2Gsc (or CamiCre), shows ectopic overexpression of synaptotagmin 2, the most efficient Ca2+ sensor for fast synchronous neurotransmitter release, in excitatory presynapses of Cre+ brains. Moreover, the upregulation of immediate-early genes and genes incorporated in bacterial artificial chromosome (BAC) transgenes, such as L-proline transporter Slc6a7, was found in Cre+ hippocampus. The copy number and integration site of the transgene are suggested to have caused the aberrant gene expression in Cre+ brains. Most importantly, CamiCre+ mice showed functional phenotypes, such as hyperactivity and enhanced associative learning, suggesting that neural activities are affected. These unexpected results suggest difficulties in interpreting results from studies using the CamiCre line and raise a warning of potential pitfalls in using Cre driver lines in general. CamiCre+ mice show the ectopic overexpression of SYT2 in excitatory presynapses CamiCre+ mice show the ectopic overexpression of SLC6A7 in hippocampal mossy fibers CamiCre+ mice show hyperactivity and enhanced associative learning Multiple copies of bacterial artificial chromosome (BAC) transgenes are integrated into the Syt2 locus
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3
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Tietz O, Cortezon-Tamarit F, Chalk R, Able S, Vallis KA. Tricyclic cell-penetrating peptides for efficient delivery of functional antibodies into cancer cells. Nat Chem 2022; 14:284-293. [PMID: 35145246 DOI: 10.1038/s41557-021-00866-0] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 11/19/2021] [Indexed: 12/13/2022]
Abstract
The intracellular environment hosts a large number of cancer- and other disease-relevant human proteins. Targeting these with internalized antibodies would allow therapeutic modulation of hitherto undruggable pathways, such as those mediated by protein-protein interactions. However, one of the major obstacles in intracellular targeting is the entrapment of biomacromolecules in the endosome. Here we report an approach to delivering antibodies and antibody fragments into the cytosol and nucleus of cells using trimeric cell-penetrating peptides (CPPs). Four trimers, based on linear and cyclic sequences of the archetypal CPP Tat, are significantly more potent than monomers and can be tuned to function by direct interaction with the plasma membrane or escape from vesicle-like bodies. These studies identify a tricyclic Tat construct that enables intracellular delivery of functional immunoglobulin-G antibodies and Fab fragments that bind intracellular targets in the cytosol and nuclei of live cells at effective concentrations as low as 1 μM.
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Affiliation(s)
- Ole Tietz
- Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, UK
| | | | - Rod Chalk
- Centre for Medicines Discovery, University of Oxford, Oxford, UK
| | - Sarah Able
- Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, UK
| | - Katherine A Vallis
- Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, UK.
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4
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Coronado-Parra T, Roldán M, Aboal M. Confocal Microscopy in Ecophysiological Studies of Algae: A Door to Understanding Autofluorescence in Red Algae. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2022; 28:218-226. [PMID: 35177134 DOI: 10.1017/s1431927621013660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Alga in the genus Chroothece have been reported mostly from aquatic or subaerial continental environments, where they grow in extreme conditions. The strain Chroothece mobilis MAESE 20.29 was exposed to different light intensities, red and green monochromatic light, ultraviolet (UV) radiation, high nitrogen concentrations, and high salinity to assess the effect of those environmental parameters on its growth. Confocal laser scanning microscopy (CLSM) was used as an “in vivo” noninvasive single-cell method for the study. The strain seemed to prefer fairly high light intensities and showed a significant increase in allophycocyanin (APC) and chlorophyll a [photosystem I (PSI) and photosystem II (PSII)] fluorescence with 330 and 789 μM/cm2/s intensities. Green monochromatic light promoted a significant increase in the fluorescence of APC and chlorophyll a (PSI and PSII). UV-A significantly decreased phycocyanin and increased APC, while UV-A + B showed a greater decreasing effect on c-Phycocyanin but did not significantly change concentrations of APC. The increase in nitrogen concentration in the culture medium significantly and negatively affected all pigments, and no effect was observed with an increase in salinity. Our data show that CLSM represents a very powerful tool for ecological research of microalgae in small volumes and may contribute to the knowledge of phycobiliproteins in vivo behavior and the parameters for the large-scale production of these pigments.
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Affiliation(s)
- Teresa Coronado-Parra
- Servicio de Microscopía del Área Científica y Técnica de Investigación (ACTI) de la Universidad de Murcia, Murcia30100, Spain
| | - Mónica Roldán
- Unidad de Microscopía Confocal e Imagen Celular, Servicio de Medicina Genética y Molecular, Instituto Pediátrico de Enfermedades Raras (IPER), Hospital Sant Joan de Déu, e Instituto de Investigación Sant Joan de Déu, Esplugues de Llobregat08950, Spain
- Institut de Recerca Sant Joan de Déu, Santa Rosa 39-57, Esplugues de Llobregat08950, Spain
| | - Marina Aboal
- Laboratorio de Algología, Facultad de Biología, Universidad de Murcia, Campus de Espinardo, MurciaE-30100, Spain
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5
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de Los Ángeles Juricic Urzúa M, Gallardo Rojas J, Couve Correa A, Cerda M, Härtel Gründler S, González-Silva C. The Dendritic Ergic: Microtubule And Actin Cytoskeletons Participate In Stop-And-Go Movement Of Mobile Carriers Between Stable Structures. Traffic 2022; 23:174-187. [PMID: 35075729 DOI: 10.1111/tra.12832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 12/30/2021] [Accepted: 01/20/2022] [Indexed: 11/29/2022]
Abstract
The ER-to-Golgi intermediate compartment (ERGIC) is a membranous organelle that mediates protein transport between the endoplasmic reticulum (ER) and the Golgi apparatus. In neurons, clusters of these vesiculotubular structures are situated throughout the cell in proximity to the ER, passing cargo to the cis-Golgi cisternae, located mainly in the perinuclear region. Although ERGIC markers have been identified in neurons, the distribution and dynamics of neuronal ERGIC structures have not been characterized yet. Here, we show that long-distance ERGIC transport occurs via an intermittent mechanism in dendrites, with mobile elements moving between stationary structures. Slow and fast live-cell imaging have captured stable ERGIC structures remaining in place over long periods of time, as well as mobile ERGIC structures advancing very short distances along dendrites. These short distances have been consistent with the lengths between the stationary ERGIC structures. Kymography revealed ERGIC elements that moved intermittently, emerging from and fusing with stationary ERGIC structures. Interestingly, this movement apparently depends not only on the integrity of the microtubule cytoskeleton, as previously reported, but on the actin cytoskeleton as well. Our results indicate that the dendritic ERGIC has a dual nature, with both stationary and mobile structures. The neural ERGIC network transports proteins via a stop-and-go movement in which both the microtubule and the actin cytoskeletons participate. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- María de Los Ángeles Juricic Urzúa
- Neuroscience Department, Facultad de Medicina, Universidad de Chile, Santiago, Chile.,Biomedical Neuroscience Institute (BNI), Santiago, Chile
| | - Javiera Gallardo Rojas
- Neuroscience Department, Facultad de Medicina, Universidad de Chile, Santiago, Chile.,Biomedical Neuroscience Institute (BNI), Santiago, Chile
| | - Andrés Couve Correa
- Neuroscience Department, Facultad de Medicina, Universidad de Chile, Santiago, Chile.,Biomedical Neuroscience Institute (BNI), Santiago, Chile
| | - Mauricio Cerda
- Biomedical Neuroscience Institute (BNI), Santiago, Chile.,Integrative Biology Program, Institute of Biomedical Sciences (ICBM), Center for Medical Informatics and Telemedicine (CIMT), Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Steffen Härtel Gründler
- Biomedical Neuroscience Institute (BNI), Santiago, Chile.,Integrative Biology Program, Institute of Biomedical Sciences (ICBM), Center for Medical Informatics and Telemedicine (CIMT), Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Carolina González-Silva
- Neuroscience Department, Facultad de Medicina, Universidad de Chile, Santiago, Chile.,Biomedical Neuroscience Institute (BNI), Santiago, Chile
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6
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Pihán P, Lisbona F, Borgonovo J, Edwards-Jorquera S, Nunes-Hasler P, Castillo K, Kepp O, Urra H, Saarnio S, Vihinen H, Carreras-Sureda A, Forveille S, Sauvat A, De Giorgis D, Pupo A, Rodríguez DA, Quarato G, Sagredo A, Lourido F, Letai A, Latorre R, Kroemer G, Demaurex N, Jokitalo E, Concha ML, Glavic Á, Green DR, Hetz C. Control of lysosomal-mediated cell death by the pH-dependent calcium channel RECS1. SCIENCE ADVANCES 2021; 7:eabe5469. [PMID: 34767445 PMCID: PMC8589314 DOI: 10.1126/sciadv.abe5469] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 09/24/2021] [Indexed: 05/27/2023]
Abstract
Programmed cell death is regulated by the balance between activating and inhibitory signals. Here, we have identified RECS1 (responsive to centrifugal force and shear stress 1) [also known as TMBIM1 (transmembrane BAX inhibitor motif containing 1)] as a proapoptotic member of the TMBIM family. In contrast to other proteins of the TMBIM family, RECS1 expression induces cell death through the canonical mitochondrial apoptosis pathway. Unbiased screening indicated that RECS1 sensitizes cells to lysosomal perturbations. RECS1 localizes to lysosomes, where it regulates their acidification and calcium content, triggering lysosomal membrane permeabilization. Structural modeling and electrophysiological studies indicated that RECS1 is a pH-regulated calcium channel, an activity that is essential to trigger cell death. RECS1 also sensitizes whole animals to stress in vivo in Drosophila melanogaster and zebrafish models. Our results unveil an unanticipated function for RECS1 as a proapoptotic component of the TMBIM family that ignites cell death programs at lysosomes.
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Affiliation(s)
- Philippe Pihán
- Biomedical Neuroscience Institute, Faculty of Medicine, University of Chile, Santiago, Chile
- Center for Geroscience, Brain Health and Metabolism (GERO), Santiago, Chile
- Program of Cellular and Molecular Biology, Institute of Biomedical Sciences, University of Chile, Santiago, Chile
| | - Fernanda Lisbona
- Biomedical Neuroscience Institute, Faculty of Medicine, University of Chile, Santiago, Chile
- Program of Cellular and Molecular Biology, Institute of Biomedical Sciences, University of Chile, Santiago, Chile
- Center for Genome Regulation, Faculty of Sciences, University of Chile, Santiago, Chile
| | - Janina Borgonovo
- Biomedical Neuroscience Institute, Faculty of Medicine, University of Chile, Santiago, Chile
- Center for Geroscience, Brain Health and Metabolism (GERO), Santiago, Chile
- Program of Integrative Biology, Institute of Biomedical Sciences, University of Chile, Santiago, Chile
| | | | - Paula Nunes-Hasler
- Department of Cell Physiology and Metabolism, University of Geneva, Geneva, Switzerland
- Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland
| | - Karen Castillo
- Centro Interdisciplinario de Neurociencia de Valparaíso, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, Chile
| | - Oliver Kepp
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue contre le cancer, Université de Paris, Sorbonne Université, Inserm U1138, Institut Universitaire de France, Paris, France
- Metabolomics and Cell Biology Platforms, Institut Gustave Roussy, Villejuif, France
| | - Hery Urra
- Biomedical Neuroscience Institute, Faculty of Medicine, University of Chile, Santiago, Chile
- Center for Geroscience, Brain Health and Metabolism (GERO), Santiago, Chile
- Program of Cellular and Molecular Biology, Institute of Biomedical Sciences, University of Chile, Santiago, Chile
| | - Suvi Saarnio
- Electron Microscopy Unit, Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Helena Vihinen
- Electron Microscopy Unit, Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Amado Carreras-Sureda
- Biomedical Neuroscience Institute, Faculty of Medicine, University of Chile, Santiago, Chile
- Center for Geroscience, Brain Health and Metabolism (GERO), Santiago, Chile
- Program of Cellular and Molecular Biology, Institute of Biomedical Sciences, University of Chile, Santiago, Chile
- Department of Cell Physiology and Metabolism, University of Geneva, Geneva, Switzerland
| | - Sabrina Forveille
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue contre le cancer, Université de Paris, Sorbonne Université, Inserm U1138, Institut Universitaire de France, Paris, France
- Metabolomics and Cell Biology Platforms, Institut Gustave Roussy, Villejuif, France
| | - Allan Sauvat
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue contre le cancer, Université de Paris, Sorbonne Université, Inserm U1138, Institut Universitaire de France, Paris, France
- Metabolomics and Cell Biology Platforms, Institut Gustave Roussy, Villejuif, France
| | - Daniela De Giorgis
- Centro Interdisciplinario de Neurociencia de Valparaíso, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, Chile
| | - Amaury Pupo
- Centro Interdisciplinario de Neurociencia de Valparaíso, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, Chile
| | - Diego A. Rodríguez
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Giovanni Quarato
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Alfredo Sagredo
- Biomedical Neuroscience Institute, Faculty of Medicine, University of Chile, Santiago, Chile
- Center for Geroscience, Brain Health and Metabolism (GERO), Santiago, Chile
- Program of Cellular and Molecular Biology, Institute of Biomedical Sciences, University of Chile, Santiago, Chile
| | - Fernanda Lourido
- Center for Genome Regulation, Faculty of Sciences, University of Chile, Santiago, Chile
| | - Anthony Letai
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Dana Building, Room DA-520, Boston, MA 02215-02115, USA
- Harvard Medical School, Boston, MA 02215, USA
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02215, USA
| | - Ramon Latorre
- Centro Interdisciplinario de Neurociencia de Valparaíso, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, Chile
| | - Guido Kroemer
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue contre le cancer, Université de Paris, Sorbonne Université, Inserm U1138, Institut Universitaire de France, Paris, France
- Metabolomics and Cell Biology Platforms, Institut Gustave Roussy, Villejuif, France
- Pôle de Biologie, Hôpital Européen Georges Pompidou, AP-HP, Paris, France
- Suzhou Institute for Systems Medicine, Chinese Academy of Medical Sciences, Suzhou, China
- Karolinska Institutet, Department of Women’s and Children’s Health, Karolinska University Hospital, Stockholm, Sweden
| | - Nicolas Demaurex
- Department of Cell Physiology and Metabolism, University of Geneva, Geneva, Switzerland
- Centro de Investigación de Estudios Avanzados, Universidad Católica del Maule, Talca, Chile
| | - Eija Jokitalo
- Electron Microscopy Unit, Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Miguel L. Concha
- Biomedical Neuroscience Institute, Faculty of Medicine, University of Chile, Santiago, Chile
- Center for Geroscience, Brain Health and Metabolism (GERO), Santiago, Chile
- Program of Integrative Biology, Institute of Biomedical Sciences, University of Chile, Santiago, Chile
| | - Álvaro Glavic
- Center for Genome Regulation, Faculty of Sciences, University of Chile, Santiago, Chile
| | - Douglas R. Green
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Claudio Hetz
- Biomedical Neuroscience Institute, Faculty of Medicine, University of Chile, Santiago, Chile
- Center for Geroscience, Brain Health and Metabolism (GERO), Santiago, Chile
- Program of Cellular and Molecular Biology, Institute of Biomedical Sciences, University of Chile, Santiago, Chile
- Buck Institute for Research on Aging, Novato, CA 94945, USA
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7
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Wan Y, Holman HA, Hansen C. Interactive Analysis for Large Volume Data from Fluorescence Microscopy at Cellular Precision. COMPUTERS & GRAPHICS 2021; 98:138-149. [PMID: 34602661 PMCID: PMC8486154 DOI: 10.1016/j.cag.2021.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The main objective for understanding fluorescence microscopy data is to investigate and evaluate the fluorescent signal intensity distributions as well as their spatial relationships across multiple channels. The quantitative analysis of 3D fluorescence microscopy data needs interactive tools for researchers to select and focus on relevant biological structures. We developed an interactive tool based on volume visualization techniques and GPU computing for streamlining rapid data analysis. Our main contribution is the implementation of common data quantification functions on streamed volumes, providing interactive analyses on large data without lengthy preprocessing. Data segmentation and quantification are coupled with brushing and executed at an interactive speed. A large volume is partitioned into data bricks, and only user-selected structures are analyzed to constrain the computational load. We designed a framework to assemble a sequence of GPU programs to handle brick borders and stitch analysis results. Our tool was developed in collaboration with domain experts and has been used to identify cell types. We demonstrate a workflow to analyze cells in vestibular epithelia of transgenic mice.
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Affiliation(s)
- Yong Wan
- The University of Utah, Salt Lake City, 84112, USA
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8
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Ferrera-González J, Francés-Soriano L, Estébanez N, Navarro-Raga E, González-Béjar M, Pérez-Prieto J. NIR laser scanning microscopy for photophysical characterization of upconversion nanoparticles and nanohybrids. NANOSCALE 2021; 13:10067-10080. [PMID: 34042932 DOI: 10.1039/d1nr00389e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Photophysical characterization of upconversion nanoparticles (UCNPs) and nanohybrids (UCNHs) is more challenging than that of down-conversion nanomaterials. Moreover, it is still difficult to gain knowledge about the homogeneity of the sample and colocalization of emissive chromophores and nanoparticles in nanohybrids. Near infrared laser scanning microscopy (NIR-LSM) is a well-known and useful imaging technique, which enables excitation in the NIR region and has been extensively applied to optical fluorescence imaging of organic fluorophores and nanomaterials, such as quantum dots, which exhibit a short-lived emission. NIR-LSM has recently been used to determine the empirical emission lifetime of UCNPs, thus extending its application range to nanomaterials with a long lifetime emission. Here, we review our previous findings and include new measurements and samples to fully address the potential of this technique. NIR-LSM has proved to be extraordinarily useful not only for photophysical characterization of UCNHs consisting of UCNPs capped with a fluorophore to easily visualize the occurrence of the resonance energy transfer process between the UCNH constituents and their homogeneity, but also to assess the colocalization of the fluorophore and the UCNP in the UCNH; all this information can be acquired on the micro-/nano-meter scale by just taking one image.
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Affiliation(s)
- Juan Ferrera-González
- Instituto de Ciencia Molecular (ICMol), Departamento de Química Orgánica, University of Valencia, C/Catedrático José Beltrán, 2, Paterna, Valencia 46980, Spain.
| | - Laura Francés-Soriano
- Instituto de Ciencia Molecular (ICMol), Departamento de Química Orgánica, University of Valencia, C/Catedrático José Beltrán, 2, Paterna, Valencia 46980, Spain. and nanoFRET.com, Laboratoire COBRA (Chimie Organique, Bioorganique, Réactivité et Analyse), Université de Rouen Normandie, CNRS, INSA, 76821 Mont-Saint-Aignan Cedex, France
| | - Nestor Estébanez
- Instituto de Ciencia Molecular (ICMol), Departamento de Química Orgánica, University of Valencia, C/Catedrático José Beltrán, 2, Paterna, Valencia 46980, Spain.
| | - Enrique Navarro-Raga
- Servicio Central de Soporte a la Investigación Experimental (SCSIE). University of Valencia, Burjassot, Valencia 46100, Spain
| | - María González-Béjar
- Instituto de Ciencia Molecular (ICMol), Departamento de Química Orgánica, University of Valencia, C/Catedrático José Beltrán, 2, Paterna, Valencia 46980, Spain.
| | - Julia Pérez-Prieto
- Instituto de Ciencia Molecular (ICMol), Departamento de Química Orgánica, University of Valencia, C/Catedrático José Beltrán, 2, Paterna, Valencia 46980, Spain.
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9
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Cornejo VH, González C, Campos M, Vargas-Saturno L, Juricic MDLÁ, Miserey-Lenkei S, Pertusa M, Madrid R, Couve A. Non-conventional Axonal Organelles Control TRPM8 Ion Channel Trafficking and Peripheral Cold Sensing. Cell Rep 2020; 30:4505-4517.e5. [DOI: 10.1016/j.celrep.2020.03.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 10/07/2019] [Accepted: 03/05/2020] [Indexed: 12/31/2022] Open
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10
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Lavancier F, Pécot T, Zengzhen L, Kervrann C. Testing independence between two random sets for the analysis of colocalization in bioimaging. Biometrics 2019; 76:36-46. [PMID: 31271216 DOI: 10.1111/biom.13115] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 06/24/2019] [Indexed: 11/30/2022]
Abstract
Colocalization aims at characterizing spatial associations between two fluorescently tagged biomolecules by quantifying the co-occurrence and correlation between the two channels acquired in fluorescence microscopy. Colocalization is presented either as the degree of overlap between the two channels or the overlays of the red and green images, with areas of yellow indicating colocalization of the molecules. This problem remains an open issue in diffraction-limited microscopy and raises new challenges with the emergence of superresolution imaging, a microscopic technique awarded by the 2014 Nobel prize in chemistry. We propose GcoPS, for Geo-coPositioning System, an original method that exploits the random sets structure of the tagged molecules to provide an explicit testing procedure. Our simulation study shows that GcoPS unequivocally outperforms the best competitive methods in adverse situations (noise, irregularly shaped fluorescent patterns, and different optical resolutions). GcoPS is also much faster, a decisive advantage to face the huge amount of data in superresolution imaging. We demonstrate the performances of GcoPS on two biological real data sets, obtained by conventional diffraction-limited microscopy technique and by superresolution technique, respectively.
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Affiliation(s)
- Frédéric Lavancier
- Laboratoire de Mathématiques Jean Leray, University of Nantes, Nantes, France
| | - Thierry Pécot
- Centre Rennes-Bretagne Atlantique, SERPICO Project Team, Inria, Rennes, France
| | - Liu Zengzhen
- CNRS UMR 144, Space Time Imaging of Endomembranes Dynamics Team, PSL Research University, Paris, France
| | - Charles Kervrann
- Centre Rennes-Bretagne Atlantique, SERPICO Project Team, Inria, Rennes, France
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11
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Apta-Smith MJ, Hernandez-Fernaud JR, Bowman AJ. Evidence for the nuclear import of histones H3.1 and H4 as monomers. EMBO J 2018; 37:embj.201798714. [PMID: 30177573 PMCID: PMC6166134 DOI: 10.15252/embj.201798714] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 07/20/2018] [Accepted: 07/25/2018] [Indexed: 11/09/2022] Open
Abstract
Newly synthesised histones are thought to dimerise in the cytosol and undergo nuclear import in complex with histone chaperones. Here, we provide evidence that human H3.1 and H4 are imported into the nucleus as monomers. Using a tether-and-release system to study the import dynamics of newly synthesised histones, we find that cytosolic H3.1 and H4 can be maintained as stable monomeric units. Cytosolically tethered histones are bound to importin-alpha proteins (predominantly IPO4), but not to histone-specific chaperones NASP, ASF1a, RbAp46 (RBBP7) or HAT1, which reside in the nucleus in interphase cells. Release of monomeric histones from their cytosolic tether results in rapid nuclear translocation, IPO4 dissociation and incorporation into chromatin at sites of replication. Quantitative analysis of histones bound to individual chaperones reveals an excess of H3 specifically associated with sNASP, suggesting that NASP maintains a soluble, monomeric pool of H3 within the nucleus and may act as a nuclear receptor for newly imported histone. In summary, we propose that histones H3 and H4 are rapidly imported as monomeric units, forming heterodimers in the nucleus rather than the cytosol.
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Affiliation(s)
| | | | - Andrew James Bowman
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, UK
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12
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IRE1α governs cytoskeleton remodelling and cell migration
through a direct interaction with filamin A. Nat Cell Biol 2018; 20:942-953. [DOI: 10.1038/s41556-018-0141-0] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 06/13/2018] [Indexed: 02/07/2023]
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13
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Jones TA, Reddy NL, Wayte SC, Adesanya O, Dimitriadis GK, Hutchinson CE, Barber TM. Brown fat depots in adult humans remain static in their locations on PET/CT despite changes in seasonality. Physiol Rep 2018; 5:5/11/e13284. [PMID: 28588036 PMCID: PMC5471433 DOI: 10.14814/phy2.13284] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 04/18/2017] [Indexed: 11/24/2022] Open
Abstract
Active brown adipose tissue (BAT) in humans has been demonstrated through use of positron emission tomography with 2-deoxy-2-(fluorine-18) fluoro-D-glucose integrated with computed tomography (18F-FDG PET/CT) scans. The aim of our study was to determine whether active human BAT depots shown on 18F-FDG PET/CT scans remain static in their location over time. This was a retrospective study. Adult human subjects (n = 15) who had had 18F-FDG PET/CT imaging (n = 38 scans in total) for clinical reasons were included on the basis of 18F-FDG uptake patterns consistent with BAT activity. For each subject, 18F-FDG BAT uptake pattern on serial 18F-FDG PET/CT images was compared to an index 18F-FDG PET/CT image with the largest demonstrable BAT volume. Object-based colocalization was expressed as Mander's correlation coefficient (where 1 = 100% overlap, 0 = no overlap). Distribution of 18F-FDG BAT activity over time and across multiple 18F-FDG BAT scans was equivalent in 60% (n = 9) of the subjects. The degree of consistency in the pattern of 18F-FDG BAT uptake in each subject over time was greater than expected by chance in 87% (n = 13) of the subjects (pair-wise agreement 75-100%, Fleiss' κ 0.4-1). The degree of BAT colocalization on serial scans was greater than that expected by chance in 93% (n = 14) of the subjects (mean Mander's coefficient 0.81 ± 0.21 [95% CI]). To our knowledge, our study provides the most conclusive evidence to date to support the notion that active BAT depots in humans (volumes and activities of which were measured through use of 18F-FDG PET/CT scans) remain static in location over sustained periods.
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Affiliation(s)
- Terence A Jones
- Clinical Sciences Research Laboratories, Warwick Medical School, University of Warwick, Coventry, CV2 2DX, United Kingdom .,Department of Radiology, University Hospitals Coventry and Warwickshire, Coventry, CV2 2DX, United Kingdom
| | - Narendra L Reddy
- Clinical Sciences Research Laboratories, Warwick Medical School, University of Warwick, Coventry, CV2 2DX, United Kingdom
| | - Sarah C Wayte
- Department of Medical Physics, University Hospitals Coventry and Warwickshire, Coventry, CV2 2DX, United Kingdom
| | - Oludolapo Adesanya
- Department of Radiology, University Hospitals Coventry and Warwickshire, Coventry, CV2 2DX, United Kingdom
| | - Georgios K Dimitriadis
- Clinical Sciences Research Laboratories, Warwick Medical School, University of Warwick, Coventry, CV2 2DX, United Kingdom
| | - Charles E Hutchinson
- Clinical Sciences Research Laboratories, Warwick Medical School, University of Warwick, Coventry, CV2 2DX, United Kingdom.,Department of Radiology, University Hospitals Coventry and Warwickshire, Coventry, CV2 2DX, United Kingdom
| | - Thomas M Barber
- Clinical Sciences Research Laboratories, Warwick Medical School, University of Warwick, Coventry, CV2 2DX, United Kingdom
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14
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Sepulveda D, Rojas-Rivera D, Rodríguez DA, Groenendyk J, Köhler A, Lebeaupin C, Ito S, Urra H, Carreras-Sureda A, Hazari Y, Vasseur-Cognet M, Ali MMU, Chevet E, Campos G, Godoy P, Vaisar T, Bailly-Maitre B, Nagata K, Michalak M, Sierralta J, Hetz C. Interactome Screening Identifies the ER Luminal Chaperone Hsp47 as a Regulator of the Unfolded Protein Response Transducer IRE1α. Mol Cell 2018; 69:238-252.e7. [PMID: 29351844 DOI: 10.1016/j.molcel.2017.12.028] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 10/05/2017] [Accepted: 12/27/2017] [Indexed: 01/17/2023]
Abstract
Maintenance of endoplasmic reticulum (ER) proteostasis is controlled by a dynamic signaling network known as the unfolded protein response (UPR). IRE1α is a major UPR transducer, determining cell fate under ER stress. We used an interactome screening to unveil several regulators of the UPR, highlighting the ER chaperone Hsp47 as the major hit. Cellular and biochemical analysis indicated that Hsp47 instigates IRE1α signaling through a physical interaction. Hsp47 directly binds to the ER luminal domain of IRE1α with high affinity, displacing the negative regulator BiP from the complex to facilitate IRE1α oligomerization. The regulation of IRE1α signaling by Hsp47 is evolutionarily conserved as validated using fly and mouse models of ER stress. Hsp47 deficiency sensitized cells and animals to experimental ER stress, revealing the significance of Hsp47 to global proteostasis maintenance. We conclude that Hsp47 adjusts IRE1α signaling by fine-tuning the threshold to engage an adaptive UPR.
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Affiliation(s)
- Denisse Sepulveda
- Biomedical Neuroscience Institute (BNI), Faculty of Medicine, University of Chile, Santiago 8380453, Chile; Center for Geroscience, Brain Health, and Metabolism (GERO), Santiago, Chile; Program of Cellular and Molecular Biology, Institute of Biomedical Sciences, University of Chile, Santiago 8380453, Chile
| | - Diego Rojas-Rivera
- Biomedical Neuroscience Institute (BNI), Faculty of Medicine, University of Chile, Santiago 8380453, Chile; Center for Geroscience, Brain Health, and Metabolism (GERO), Santiago, Chile; Program of Cellular and Molecular Biology, Institute of Biomedical Sciences, University of Chile, Santiago 8380453, Chile
| | - Diego A Rodríguez
- Biomedical Neuroscience Institute (BNI), Faculty of Medicine, University of Chile, Santiago 8380453, Chile; Program of Cellular and Molecular Biology, Institute of Biomedical Sciences, University of Chile, Santiago 8380453, Chile; Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jody Groenendyk
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2S7, Canada
| | - Andres Köhler
- Biomedical Neuroscience Institute (BNI), Faculty of Medicine, University of Chile, Santiago 8380453, Chile; Program of Physiology and Biophysics, Institute of Biomedical Sciences, University of Chile, Santiago 8380453, Chile
| | | | - Shinya Ito
- Department of Molecular Biosciences, Faculty of Life Sciences, Kyoto and Sangyo University, Motoyama, Kamigamo, Kita-ku, Kyoto 603-8555, Japan
| | - Hery Urra
- Biomedical Neuroscience Institute (BNI), Faculty of Medicine, University of Chile, Santiago 8380453, Chile; Center for Geroscience, Brain Health, and Metabolism (GERO), Santiago, Chile; Program of Cellular and Molecular Biology, Institute of Biomedical Sciences, University of Chile, Santiago 8380453, Chile
| | - Amado Carreras-Sureda
- Biomedical Neuroscience Institute (BNI), Faculty of Medicine, University of Chile, Santiago 8380453, Chile; Center for Geroscience, Brain Health, and Metabolism (GERO), Santiago, Chile; Program of Cellular and Molecular Biology, Institute of Biomedical Sciences, University of Chile, Santiago 8380453, Chile
| | - Younis Hazari
- Biomedical Neuroscience Institute (BNI), Faculty of Medicine, University of Chile, Santiago 8380453, Chile; Center for Geroscience, Brain Health, and Metabolism (GERO), Santiago, Chile; Program of Cellular and Molecular Biology, Institute of Biomedical Sciences, University of Chile, Santiago 8380453, Chile
| | - Mireille Vasseur-Cognet
- Institut d'Ecologie et des Sciences de l'Environnement de Paris, Bondy; Sorbonne Universités, and Institut National de la Santé et de la Recherche Médicale, Paris 7 113, France
| | - Maruf M U Ali
- Department of Life Sciences, Imperial College, London SW7 2AZ, UK
| | - Eric Chevet
- Inserm U1242, Chemistry, Oncogenesis, Stress, & Signaling, University of Rennes 1, F-35000 Rennes, France; Centre de Lutte le Cancer Eugène Marquis, F-35000 Rennes, France
| | - Gisela Campos
- IfADo-Leibniz Research Centre for Working Environment and Human Factors at the Technical University Dortmund, Dortmund 44139, Germany
| | - Patricio Godoy
- IfADo-Leibniz Research Centre for Working Environment and Human Factors at the Technical University Dortmund, Dortmund 44139, Germany
| | - Tomas Vaisar
- Division of Metabolism, Endocrinology and Nutrition, University of Washington School of Medicine, Seattle, WA 98195, USA
| | | | - Kazuhiro Nagata
- Department of Molecular Biosciences, Faculty of Life Sciences, Kyoto and Sangyo University, Motoyama, Kamigamo, Kita-ku, Kyoto 603-8555, Japan
| | - Marek Michalak
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2S7, Canada
| | - Jimena Sierralta
- Biomedical Neuroscience Institute (BNI), Faculty of Medicine, University of Chile, Santiago 8380453, Chile; Program of Physiology and Biophysics, Institute of Biomedical Sciences, University of Chile, Santiago 8380453, Chile
| | - Claudio Hetz
- Biomedical Neuroscience Institute (BNI), Faculty of Medicine, University of Chile, Santiago 8380453, Chile; Center for Geroscience, Brain Health, and Metabolism (GERO), Santiago, Chile; Program of Cellular and Molecular Biology, Institute of Biomedical Sciences, University of Chile, Santiago 8380453, Chile; Buck Institute for Research on Aging, Novato, CA 94945, USA; Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston MA 02115, USA.
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15
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Duran-Aniotz C, Cornejo VH, Espinoza S, Ardiles ÁO, Medinas DB, Salazar C, Foley A, Gajardo I, Thielen P, Iwawaki T, Scheper W, Soto C, Palacios AG, Hoozemans JJM, Hetz C. IRE1 signaling exacerbates Alzheimer's disease pathogenesis. Acta Neuropathol 2017; 134:489-506. [PMID: 28341998 DOI: 10.1007/s00401-017-1694-x] [Citation(s) in RCA: 138] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 03/07/2017] [Accepted: 03/07/2017] [Indexed: 12/19/2022]
Abstract
Altered proteostasis is a salient feature of Alzheimer's disease (AD), highlighting the occurrence of endoplasmic reticulum (ER) stress and abnormal protein aggregation. ER stress triggers the activation of the unfolded protein response (UPR), a signaling pathway that enforces adaptive programs to sustain proteostasis or eliminate terminally damaged cells. IRE1 is an ER-located kinase and endoribonuclease that operates as a major stress transducer, mediating both adaptive and proapoptotic programs under ER stress. IRE1 signaling controls the expression of the transcription factor XBP1, in addition to degrade several RNAs. Importantly, a polymorphism in the XBP1 promoter was suggested as a risk factor to develop AD. Here, we demonstrate a positive correlation between the progression of AD histopathology and the activation of IRE1 in human brain tissue. To define the significance of the UPR to AD, we targeted IRE1 expression in a transgenic mouse model of AD. Despite initial expectations that IRE1 signaling may protect against AD, genetic ablation of the RNase domain of IRE1 in the nervous system significantly reduced amyloid deposition, the content of amyloid β oligomers, and astrocyte activation. IRE1 deficiency fully restored the learning and memory capacity of AD mice, associated with improved synaptic function and improved long-term potentiation (LTP). At the molecular level, IRE1 deletion reduced the expression of amyloid precursor protein (APP) in cortical and hippocampal areas of AD mice. In vitro experiments demonstrated that inhibition of IRE1 downstream signaling reduces APP steady-state levels, associated with its retention at the ER followed by proteasome-mediated degradation. Our findings uncovered an unanticipated role of IRE1 in the pathogenesis of AD, offering a novel target for disease intervention.
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Affiliation(s)
- Claudia Duran-Aniotz
- Faculty of Medicine, Biomedical Neuroscience Institute, University of Chile, Santiago, Chile
- Center for Geroscience, Brain Health and Metabolism, Santiago, Chile
- Program of Cellular and Molecular Biology, Institute of Biomedical Sciences (Sector B, second floor), University of Chile, Independencia 1027, P.O.BOX 70086, Santiago, Chile
| | - Victor Hugo Cornejo
- Faculty of Medicine, Biomedical Neuroscience Institute, University of Chile, Santiago, Chile
- Center for Geroscience, Brain Health and Metabolism, Santiago, Chile
- Program of Cellular and Molecular Biology, Institute of Biomedical Sciences (Sector B, second floor), University of Chile, Independencia 1027, P.O.BOX 70086, Santiago, Chile
| | - Sandra Espinoza
- Faculty of Medicine, Biomedical Neuroscience Institute, University of Chile, Santiago, Chile
- Center for Geroscience, Brain Health and Metabolism, Santiago, Chile
- Program of Cellular and Molecular Biology, Institute of Biomedical Sciences (Sector B, second floor), University of Chile, Independencia 1027, P.O.BOX 70086, Santiago, Chile
| | - Álvaro O Ardiles
- Centro Interdisciplinario de Neurociencia de Valparaiso, Universidad de Valparaiso, Valparaiso, Chile
| | - Danilo B Medinas
- Faculty of Medicine, Biomedical Neuroscience Institute, University of Chile, Santiago, Chile
- Center for Geroscience, Brain Health and Metabolism, Santiago, Chile
- Program of Cellular and Molecular Biology, Institute of Biomedical Sciences (Sector B, second floor), University of Chile, Independencia 1027, P.O.BOX 70086, Santiago, Chile
| | - Claudia Salazar
- Centro Interdisciplinario de Neurociencia de Valparaiso, Universidad de Valparaiso, Valparaiso, Chile
| | - Andrew Foley
- Faculty of Medicine, Biomedical Neuroscience Institute, University of Chile, Santiago, Chile
- Program of Cellular and Molecular Biology, Institute of Biomedical Sciences (Sector B, second floor), University of Chile, Independencia 1027, P.O.BOX 70086, Santiago, Chile
| | - Ivana Gajardo
- Centro Interdisciplinario de Neurociencia de Valparaiso, Universidad de Valparaiso, Valparaiso, Chile
| | - Peter Thielen
- Department of Immunology and Infectious diseases, Harvard School of Public Health, Boston, MA, USA
| | - Takao Iwawaki
- Division of Cell Medicine, Department of Life Science, Medical Research Institute, Kanazawa Medical University, 1-1 Daigaku, Uchinada, Kahoku, Ishikawa, 920-0293, Japan
| | - Wiep Scheper
- Department of Clinical Genetics and Alzheimer Center, VU University Medical Center, Amsterdam, The Netherlands
- Department of Functional Genomics, Center for Neurogenomics and Cognitive Research, VU University, Amsterdam, The Netherlands
| | - Claudio Soto
- Department of Neurology, Mitchell Center for Alzheimer's disease and Related Brain Disorders, The University of Texas Houston Medical School at Houston, Houston, TX, 77030, USA
| | - Adrian G Palacios
- Centro Interdisciplinario de Neurociencia de Valparaiso, Universidad de Valparaiso, Valparaiso, Chile
| | - Jeroen J M Hoozemans
- Department of Pathology, VU University Medical Center, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Claudio Hetz
- Faculty of Medicine, Biomedical Neuroscience Institute, University of Chile, Santiago, Chile.
- Center for Geroscience, Brain Health and Metabolism, Santiago, Chile.
- Program of Cellular and Molecular Biology, Institute of Biomedical Sciences (Sector B, second floor), University of Chile, Independencia 1027, P.O.BOX 70086, Santiago, Chile.
- Department of Immunology and Infectious diseases, Harvard School of Public Health, Boston, MA, USA.
- Buck Institute for Research on Aging, Novato, CA, 94945, USA.
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16
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Ulman V, Svoboda D, Nykter M, Kozubek M, Ruusuvuori P. Virtual cell imaging: A review on simulation methods employed in image cytometry. Cytometry A 2016; 89:1057-1072. [PMID: 27922735 DOI: 10.1002/cyto.a.23031] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 07/20/2016] [Accepted: 11/14/2016] [Indexed: 02/03/2023]
Abstract
The simulations of cells and microscope images thereof have been used to facilitate the development, selection, and validation of image analysis algorithms employed in cytometry as well as for modeling and understanding cell structure and dynamics beyond what is visible in the eyepiece. The simulation approaches vary from simple parametric models of specific cell components-especially shapes of cells and cell nuclei-to learning-based synthesis and multi-stage simulation models for complex scenes that simultaneously visualize multiple object types and incorporate various properties of the imaged objects and laws of image formation. This review covers advances in artificial digital cell generation at scales ranging from particles up to tissue synthesis and microscope image simulation methods, provides examples of the use of simulated images for various purposes ranging from subcellular object detection to cell tracking, and discusses how such simulators have been validated. Finally, the future possibilities and limitations of simulation-based validation are considered. © 2016 International Society for Advancement of Cytometry.
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Affiliation(s)
- Vladimír Ulman
- Centre for Biomedical Image Analysis, Faculty of Informatics, Masaryk University, Brno, Czech Republic
| | - David Svoboda
- Centre for Biomedical Image Analysis, Faculty of Informatics, Masaryk University, Brno, Czech Republic
| | - Matti Nykter
- Institute of Biosciences and Medical Technology - BioMediTech, University of Tampere, Tampere, Finland
| | - Michal Kozubek
- Centre for Biomedical Image Analysis, Faculty of Informatics, Masaryk University, Brno, Czech Republic
| | - Pekka Ruusuvuori
- Institute of Biosciences and Medical Technology - BioMediTech, University of Tampere, Tampere, Finland.,Pori Campus, Tampere University of Technology, Pori, Finland
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17
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Pastorek L, Sobol M, Hozák P. Colocalization coefficients evaluating the distribution of molecular targets in microscopy methods based on pointed patterns. Histochem Cell Biol 2016; 146:391-406. [PMID: 27460592 PMCID: PMC5037163 DOI: 10.1007/s00418-016-1467-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/13/2016] [Indexed: 01/28/2023]
Abstract
In biomedical studies, the colocalization is commonly understood as the overlap between distinctive labelings in images. This term is usually associated especially with quantitative evaluation of the immunostaining in fluorescence microscopy. On the other hand, the evaluation of the immunolabeling colocalization in the electron microscopy images is still under-investigated and biased by the subjective and non-quantitative interpretation of the image data. We introduce a novel computational technique for quantifying the level of colocalization in pointed patterns. Our approach follows the idea included in the widely used Manders' colocalization coefficients in fluorescence microscopy and represents its counterpart for electron microscopy. In presented methodology, colocalization is understood as the product of the spatial interactions at the single-particle (single-molecule) level. Our approach extends the current significance testing in the immunoelectron microscopy images and establishes the descriptive colocalization coefficients. To demonstrate the performance of the proposed coefficients, we investigated the level of spatial interactions of phosphatidylinositol 4,5-bisphosphate with fibrillarin in nucleoli. We compared the electron microscopy colocalization coefficients with Manders' colocalization coefficients for confocal microscopy and super-resolution structured illumination microscopy. The similar tendency of the values obtained using different colocalization approaches suggests the biological validity of the scientific conclusions. The presented methodology represents a good basis for further development of the quantitative analysis of immunoelectron microscopy data and can be used for studying molecular interactions at the ultrastructural level. Moreover, this methodology can be applied also to the other super-resolution microscopy techniques focused on characterization of discrete pointed structures.
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Affiliation(s)
- Lukáš Pastorek
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics ASCR v.v.i., Vídeňská 1083, 142 20, Prague 4, Czech Republic
- Microscopy Centre, Institute of Molecular Genetics ASCR v.v.i., Vídeňská 1083, 142 20, Prague 4, Czech Republic
| | - Margarita Sobol
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics ASCR v.v.i., Vídeňská 1083, 142 20, Prague 4, Czech Republic
- Microscopy Centre, Institute of Molecular Genetics ASCR v.v.i., Vídeňská 1083, 142 20, Prague 4, Czech Republic
| | - Pavel Hozák
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics ASCR v.v.i., Vídeňská 1083, 142 20, Prague 4, Czech Republic.
- Microscopy Centre, Institute of Molecular Genetics ASCR v.v.i., Vídeňská 1083, 142 20, Prague 4, Czech Republic.
- Laboratory of Epigenetics of the Cell Nucleus, Division BIOCEV, Institute of Molecular Genetics of the ASCR v. v. i., Průmyslová 595, 252 50, Vestec, Czech Republic.
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18
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Covarrubias-Pinto A, Moll P, Solís-Maldonado M, Acuña AI, Riveros A, Miró MP, Papic E, Beltrán FA, Cepeda C, Concha II, Brauchi S, Castro MA. Beyond the redox imbalance: Oxidative stress contributes to an impaired GLUT3 modulation in Huntington's disease. Free Radic Biol Med 2015; 89:1085-96. [PMID: 26456058 PMCID: PMC4840472 DOI: 10.1016/j.freeradbiomed.2015.09.024] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 08/31/2015] [Accepted: 09/01/2015] [Indexed: 11/29/2022]
Abstract
Failure in energy metabolism and oxidative damage are associated with Huntington's disease (HD). Ascorbic acid released during synaptic activity inhibits use of neuronal glucose, favouring lactate uptake to sustain brain activity. Here, we observe a decreased expression of GLUT3 in STHdhQ111 cells (HD cells) and R6/2 mice (HD mice). Localisation of GLUT3 is decreased at the plasma membrane in HD cells affecting the modulation of glucose uptake by ascorbic acid. An ascorbic acid analogue without antioxidant activity is able to inhibit glucose uptake in HD cells. The impaired modulation of glucose uptake by ascorbic acid is directly related to ROS levels indicating that oxidative stress sequesters the ability of ascorbic acid to modulate glucose utilisation. Therefore, in HD, a decrease in GLUT3 localisation at the plasma membrane would contribute to an altered neuronal glucose uptake during resting periods while redox imbalance should contribute to metabolic failure during synaptic activity.
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Affiliation(s)
- Adriana Covarrubias-Pinto
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile; Center for Interdisciplinary Studies on the Nervous system (CISNe), Universidad Austral de Chile, Valdivia, Chile
| | - Pablo Moll
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile; Center for Interdisciplinary Studies on the Nervous system (CISNe), Universidad Austral de Chile, Valdivia, Chile
| | - Macarena Solís-Maldonado
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile; Center for Interdisciplinary Studies on the Nervous system (CISNe), Universidad Austral de Chile, Valdivia, Chile
| | - Aníbal I Acuña
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile; Center for Interdisciplinary Studies on the Nervous system (CISNe), Universidad Austral de Chile, Valdivia, Chile
| | - Andrea Riveros
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile; Center for Interdisciplinary Studies on the Nervous system (CISNe), Universidad Austral de Chile, Valdivia, Chile
| | - María Paz Miró
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile; Center for Interdisciplinary Studies on the Nervous system (CISNe), Universidad Austral de Chile, Valdivia, Chile
| | - Eduardo Papic
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile; Center for Interdisciplinary Studies on the Nervous system (CISNe), Universidad Austral de Chile, Valdivia, Chile
| | - Felipe A Beltrán
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile; Center for Interdisciplinary Studies on the Nervous system (CISNe), Universidad Austral de Chile, Valdivia, Chile
| | - Carlos Cepeda
- Intellectual and Developmental Disabilities Research Center, Semel Institute for Neuroscience and Human Behavior, Brain Research Institute, The David Geffen School of Medicine, UCLA, Los Angeles, USA and
| | - Ilona I Concha
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Sebastián Brauchi
- Center for Interdisciplinary Studies on the Nervous system (CISNe), Universidad Austral de Chile, Valdivia, Chile; Instituto de Fisiología, Facultad de Medicina, Universidad Austral de Chile, Valdivia, Chile
| | - Maite A Castro
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile; Center for Interdisciplinary Studies on the Nervous system (CISNe), Universidad Austral de Chile, Valdivia, Chile.
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19
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Colocalization Estimation Using Graphical Modeling and Variational Bayesian Expectation Maximization: Towards a Parameter-Free Approach. ACTA ACUST UNITED AC 2015. [PMID: 26221663 DOI: 10.1007/978-3-319-19992-4_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
In microscopy imaging, colocalization between two biological entities (e.g., protein-protein or protein-cell) refers to the (stochastic) dependencies between the spatial locations of the two entities in the biological specimen. Measuring colocalization between two entities relies on fluorescence imaging of the specimen using two fluorescent chemicals, each of which indicates the presence/absence of one of the entities at any pixel location. State-of-the-art methods for estimating colocalization rely on post-processing image data using an adhoc sequence of algorithms with many free parameters that are tuned visually. This leads to loss of reproducibility of the results. This paper proposes a brand-new framework for estimating the nature and strength of colocalization directly from corrupted image data by solving a single unified optimization problem that automatically deals with noise, object labeling, and parameter tuning. The proposed framework relies on probabilistic graphical image modeling and a novel inference scheme using variational Bayesian expectation maximization for estimating all model parameters, including colocalization, from data. Results on simulated and real-world data demonstrate improved performance over the state of the art.
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20
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Gemble S, Ahuja A, Buhagiar-Labarchède G, Onclercq-Delic R, Dairou J, Biard DSF, Lambert S, Lopes M, Amor-Guéret M. Pyrimidine Pool Disequilibrium Induced by a Cytidine Deaminase Deficiency Inhibits PARP-1 Activity, Leading to the Under Replication of DNA. PLoS Genet 2015; 11:e1005384. [PMID: 26181065 PMCID: PMC4504519 DOI: 10.1371/journal.pgen.1005384] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 06/23/2015] [Indexed: 12/31/2022] Open
Abstract
Genome stability is jeopardized by imbalances of the dNTP pool; such imbalances affect the rate of fork progression. For example, cytidine deaminase (CDA) deficiency leads to an excess of dCTP, slowing the replication fork. We describe here a novel mechanism by which pyrimidine pool disequilibrium compromises the completion of replication and chromosome segregation: the intracellular accumulation of dCTP inhibits PARP-1 activity. CDA deficiency results in incomplete DNA replication when cells enter mitosis, leading to the formation of ultrafine anaphase bridges between sister-chromatids at "difficult-to-replicate" sites such as centromeres and fragile sites. Using molecular combing, electron microscopy and a sensitive assay involving cell imaging to quantify steady-state PAR levels, we found that DNA replication was unsuccessful due to the partial inhibition of basal PARP-1 activity, rather than slower fork speed. The stimulation of PARP-1 activity in CDA-deficient cells restores replication and, thus, chromosome segregation. Moreover, increasing intracellular dCTP levels generates under-replication-induced sister-chromatid bridges as efficiently as PARP-1 knockdown. These results have direct implications for Bloom syndrome (BS), a rare genetic disease combining susceptibility to cancer and genomic instability. BS results from mutation of the BLM gene, encoding BLM, a RecQ 3'-5' DNA helicase, a deficiency of which leads to CDA downregulation. BS cells thus have a CDA defect, resulting in a high frequency of ultrafine anaphase bridges due entirely to dCTP-dependent PARP-1 inhibition and independent of BLM status. Our study describes previously unknown pathological consequences of the distortion of dNTP pools and reveals an unexpected role for PARP-1 in preventing DNA under-replication and chromosome segregation defects.
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Affiliation(s)
- Simon Gemble
- Institut Curie, Centre de Recherche, Orsay, France
- CNRS UMR 3348, Stress Génotoxiques et Cancer, Centre Universitaire, Orsay, France
| | - Akshay Ahuja
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Géraldine Buhagiar-Labarchède
- Institut Curie, Centre de Recherche, Orsay, France
- CNRS UMR 3348, Stress Génotoxiques et Cancer, Centre Universitaire, Orsay, France
| | - Rosine Onclercq-Delic
- Institut Curie, Centre de Recherche, Orsay, France
- CNRS UMR 3348, Stress Génotoxiques et Cancer, Centre Universitaire, Orsay, France
| | - Julien Dairou
- Université Paris Diderot, Sorbonne Paris Cité, Unité de Biologie Fonctionnelle et Adaptative (BFA) UMR 8251 CNRS, Plateforme Bioprofiler Bâtiment Buffon, 346A Case 7073, Paris, France
| | | | - Sarah Lambert
- Institut Curie, Centre de Recherche, Orsay, France
- CNRS UMR 3348, Stress Génotoxiques et Cancer, Centre Universitaire, Orsay, France
| | - Massimo Lopes
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Mounira Amor-Guéret
- Institut Curie, Centre de Recherche, Orsay, France
- CNRS UMR 3348, Stress Génotoxiques et Cancer, Centre Universitaire, Orsay, France
- * E-mail:
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21
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Dorgau B, Herrling R, Schultz K, Greb H, Segelken J, Ströh S, Bolte P, Weiler R, Dedek K, Janssen-Bienhold U. Connexin50 couples axon terminals of mouse horizontal cells by homotypic gap junctions. J Comp Neurol 2015; 523:2062-81. [PMID: 25823610 DOI: 10.1002/cne.23779] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Revised: 02/12/2015] [Accepted: 03/24/2015] [Indexed: 11/06/2022]
Abstract
Horizontal cells in the mouse retina are of the axon-bearing B-type and contribute to the gain control of photoreceptors and to the center-surround organization of bipolar cells by providing feedback and feedforward signals to photoreceptors and bipolar cells, respectively. Horizontal cells form two independent networks, coupled by dendro-dendritic and axo-axonal gap junctions composed of connexin57 (Cx57). In Cx57-deficient mice, occasionally the residual tracer coupling of horizontal cell somata was observed. Also, negative feedback from horizontal cells to photoreceptors, potentially mediated by connexin hemichannels, appeared unaffected. These results point to the expression of a second connexin in mouse horizontal cells. We investigated the expression of Cx50, which was recently identified in axonless A-type horizontal cells of the rabbit retina. In the mouse retina, Cx50-immunoreactive puncta were predominantly localized on large axon terminals of horizontal cells. Electron microscopy did not reveal any Cx50-immunolabeling at the membrane of horizontal cell tips invaginating photoreceptor terminals, ruling out the involvement of Cx50 in negative feedback. Moreover, Cx50 colocalized only rarely with Cx57 on horizontal cell processes, indicating that both connexins form homotypic rather than heterotypic or heteromeric gap junctions. To check whether the expression of Cx50 is changed when Cx57 is lacking, we compared the Cx50 expression in wildtype and Cx57-deficient mice. However, Cx50 expression was unaffected in Cx57-deficient mice. In summary, our results indicate that horizontal cell axon terminals form two independent sets of homotypic gap junctions, a feature which might be important for light adaptation in the retina.
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Affiliation(s)
- Birthe Dorgau
- Department of Neurobiology, University of Oldenburg, D-26111, Oldenburg, Germany.,Institute of Genetic Medicine, Newcastle University, Newcastle, UK
| | - Regina Herrling
- Department of Neurobiology, University of Oldenburg, D-26111, Oldenburg, Germany
| | - Konrad Schultz
- Department of Neurobiology, University of Oldenburg, D-26111, Oldenburg, Germany
| | - Helena Greb
- Department of Neurobiology, University of Oldenburg, D-26111, Oldenburg, Germany
| | - Jasmin Segelken
- Department of Neurobiology, University of Oldenburg, D-26111, Oldenburg, Germany
| | - Sebastian Ströh
- Institute of Genetic Medicine, Newcastle University, Newcastle, UK
| | - Petra Bolte
- Institute of Genetic Medicine, Newcastle University, Newcastle, UK.,Animal Navigation, University of Oldenburg, Oldenburg, Germany
| | | | - Karin Dedek
- Department of Neurobiology, University of Oldenburg, D-26111, Oldenburg, Germany
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22
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Lagache T, Sauvonnet N, Danglot L, Olivo-Marin JC. Statistical analysis of molecule colocalization in bioimaging. Cytometry A 2015; 87:568-79. [PMID: 25605428 DOI: 10.1002/cyto.a.22629] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 12/19/2014] [Accepted: 12/28/2014] [Indexed: 12/15/2022]
Abstract
The quantitative analysis of molecule interactions in bioimaging is key for understanding the molecular orchestration of cellular processes and is generally achieved through the study of the spatial colocalization between the different populations of molecules. Colocalization methods are traditionally divided into pixel-based methods that measure global correlation coefficients from the overlap between pixel intensities in different color channels, and object-based methods that first segment molecule spots and then analyze their spatial distributions with second-order statistics. Here, we present a review of such colocalization methods and give a quantitative comparison of their relative merits in different types of biological applications and contexts. We show on synthetic and biological images that object-based methods are more robust statistically than pixel-based methods, and allow moreover to quantify accurately the number of colocalized molecules.
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Affiliation(s)
- Thibault Lagache
- Cell Biology and Infection Department, BioImage Analysis Unit, Institut Pasteur, 75724 Paris Cedex 15, France
| | - Nathalie Sauvonnet
- Cell Biology and Infection Department, Molecular Microbial Pathogenesis Unit, Institut Pasteur, 75724 Paris Cedex 15, France
| | - Lydia Danglot
- Membrane Traffic in Heath and Disease Unit - Inserm 950. Institut Jacques Monod - CNRS UMR7592, Université Paris Diderot, 75205 Paris Cedex 13, France
| | - Jean-Christophe Olivo-Marin
- Cell Biology and Infection Department, BioImage Analysis Unit, Institut Pasteur, 75724 Paris Cedex 15, France
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23
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Humpert F, Yahiatène I, Lummer M, Sauer M, Huser T. Quantifying molecular colocalization in live cell fluorescence microscopy. JOURNAL OF BIOPHOTONICS 2015; 8:124-132. [PMID: 24375988 DOI: 10.1002/jbio.201300146] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Revised: 11/18/2013] [Accepted: 11/19/2013] [Indexed: 06/03/2023]
Abstract
One of the most challenging tasks in microscopy is the quantitative identification and characterization of molecular interactions. In living cells this task is typically performed by fluorescent labeling of the interaction partners with spectrally distinct fluorophores and imaging in different color channels. Current methods for determining colocalization of molecules result in outcomes that can vary greatly depending on signal-to-noise ratios, threshold and background levels, or differences in intensity between channels. Here, we present a novel and quantitative method for determining the degree of colocalization in live-cell fluorescence microscopy images for two and more data channels. Moreover, our method enables the construction of images that directly classify areas of high colocalization.
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Affiliation(s)
- Fabian Humpert
- Department of Physics, University of Bielefeld, Bielefeld, Germany
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24
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Pennanen C, Parra V, López-Crisosto C, Morales PE, Del Campo A, Gutierrez T, Rivera-Mejías P, Kuzmicic J, Chiong M, Zorzano A, Rothermel BA, Lavandero S. Mitochondrial fission is required for cardiomyocyte hypertrophy mediated by a Ca2+-calcineurin signaling pathway. J Cell Sci 2014; 127:2659-71. [PMID: 24777478 PMCID: PMC4058110 DOI: 10.1242/jcs.139394] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Accepted: 03/20/2014] [Indexed: 12/12/2022] Open
Abstract
Cardiomyocyte hypertrophy has been associated with diminished mitochondrial metabolism. Mitochondria are crucial organelles for the production of ATP, and their morphology and function are regulated by the dynamic processes of fusion and fission. The relationship between mitochondrial dynamics and cardiomyocyte hypertrophy is still poorly understood. Here, we show that treatment of cultured neonatal rat cardiomyocytes with the hypertrophic agonist norepinephrine promotes mitochondrial fission (characterized by a decrease in mitochondrial mean volume and an increase in the relative number of mitochondria per cell) and a decrease in mitochondrial function. We demonstrate that norepinephrine acts through α1-adrenergic receptors to increase cytoplasmic Ca(2+), activating calcineurin and promoting migration of the fission protein Drp1 (encoded by Dnml1) to mitochondria. Dominant-negative Drp1 (K38A) not only prevented mitochondrial fission, it also blocked hypertrophic growth of cardiomyocytes in response to norepinephrine. Remarkably, an antisense adenovirus against the fusion protein Mfn2 (AsMfn2) was sufficient to increase mitochondrial fission and stimulate a hypertrophic response without agonist treatment. Collectively, these results demonstrate the importance of mitochondrial dynamics in the development of cardiomyocyte hypertrophy and metabolic remodeling.
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Affiliation(s)
- Christian Pennanen
- Advanced Center for Chronic Diseases (ACCDiS), Universidad de Chile, Santiago 8380492, Chile Centro Estudios Moleculares de la Celula, Facultad Ciencias Quimicas y Farmaceuticas & Facultad Medicina, Universidad de Chile, Santiago 8380492, Chile
| | - Valentina Parra
- Advanced Center for Chronic Diseases (ACCDiS), Universidad de Chile, Santiago 8380492, Chile Centro Estudios Moleculares de la Celula, Facultad Ciencias Quimicas y Farmaceuticas & Facultad Medicina, Universidad de Chile, Santiago 8380492, Chile Department of Internal Medicine (Cardiology Division), University of Texas Southwestern Medical Center, Dallas, TX 75235, USA
| | - Camila López-Crisosto
- Advanced Center for Chronic Diseases (ACCDiS), Universidad de Chile, Santiago 8380492, Chile Centro Estudios Moleculares de la Celula, Facultad Ciencias Quimicas y Farmaceuticas & Facultad Medicina, Universidad de Chile, Santiago 8380492, Chile
| | - Pablo E Morales
- Advanced Center for Chronic Diseases (ACCDiS), Universidad de Chile, Santiago 8380492, Chile Centro Estudios Moleculares de la Celula, Facultad Ciencias Quimicas y Farmaceuticas & Facultad Medicina, Universidad de Chile, Santiago 8380492, Chile
| | - Andrea Del Campo
- Advanced Center for Chronic Diseases (ACCDiS), Universidad de Chile, Santiago 8380492, Chile Centro Estudios Moleculares de la Celula, Facultad Ciencias Quimicas y Farmaceuticas & Facultad Medicina, Universidad de Chile, Santiago 8380492, Chile
| | - Tomás Gutierrez
- Advanced Center for Chronic Diseases (ACCDiS), Universidad de Chile, Santiago 8380492, Chile Centro Estudios Moleculares de la Celula, Facultad Ciencias Quimicas y Farmaceuticas & Facultad Medicina, Universidad de Chile, Santiago 8380492, Chile
| | - Pablo Rivera-Mejías
- Advanced Center for Chronic Diseases (ACCDiS), Universidad de Chile, Santiago 8380492, Chile Centro Estudios Moleculares de la Celula, Facultad Ciencias Quimicas y Farmaceuticas & Facultad Medicina, Universidad de Chile, Santiago 8380492, Chile
| | - Jovan Kuzmicic
- Advanced Center for Chronic Diseases (ACCDiS), Universidad de Chile, Santiago 8380492, Chile Centro Estudios Moleculares de la Celula, Facultad Ciencias Quimicas y Farmaceuticas & Facultad Medicina, Universidad de Chile, Santiago 8380492, Chile
| | - Mario Chiong
- Advanced Center for Chronic Diseases (ACCDiS), Universidad de Chile, Santiago 8380492, Chile Centro Estudios Moleculares de la Celula, Facultad Ciencias Quimicas y Farmaceuticas & Facultad Medicina, Universidad de Chile, Santiago 8380492, Chile
| | - Antonio Zorzano
- Institute for Research in Biomedicine (IRB), 08028 Barcelona, Spain Departamento de Bioquímica í Biología molecular, Facultat de Biología, Universitat de Barcelona, Barcelona, Spain CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, Spain
| | - Beverly A Rothermel
- Department of Internal Medicine (Cardiology Division), University of Texas Southwestern Medical Center, Dallas, TX 75235, USA
| | - Sergio Lavandero
- Advanced Center for Chronic Diseases (ACCDiS), Universidad de Chile, Santiago 8380492, Chile Centro Estudios Moleculares de la Celula, Facultad Ciencias Quimicas y Farmaceuticas & Facultad Medicina, Universidad de Chile, Santiago 8380492, Chile Department of Internal Medicine (Cardiology Division), University of Texas Southwestern Medical Center, Dallas, TX 75235, USA
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Valenzuela JI, Jaureguiberry-Bravo M, Salas DA, Ramírez OA, Cornejo VH, Lu HE, Blanpied TA, Couve A. Transport along the dendritic endoplasmic reticulum mediates the trafficking of GABAB receptors. J Cell Sci 2014; 127:3382-95. [PMID: 24895402 DOI: 10.1242/jcs.151092] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
In neurons, secretory organelles within the cell body are complemented by the dendritic endoplasmic reticulum (ER) and Golgi outposts (GOPs), whose role in neurotransmitter receptor trafficking is poorly understood. γ-aminobutyric acid (GABA) type B metabotropic receptors (GABABRs) regulate the efficacy of synaptic transmission throughout the brain. Their plasma membrane availability is controlled by mechanisms involving an ER retention motif and assembly-dependent ER export. Thus, they constitute an ideal molecular model to study ER trafficking, but the extent to which the dendritic ER participates in GABABR biosynthesis has not been thoroughly explored. Here, we show that GABAB1 localizes preferentially to the ER in dendrites and moves long distances within this compartment. Not only diffusion but also microtubule and dynein-dependent mechanisms control dendritic ER transport. GABABRs insert throughout the somatodendritic plasma membrane but dendritic post-ER carriers containing GABABRs do not fuse selectively with GOPs. This study furthers our understanding of the spatial selectivity of neurotransmitter receptors for dendritic organelles.
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Affiliation(s)
- José I Valenzuela
- Program of Physiology and Biophysics, ICBM, Faculty of Medicine, Universidad de Chile, Santiago CP8380453, Chile Biomedical Neuroscience Institute, BNI, Faculty of Medicine, Universidad de Chile, Santiago CP8380453, Chile
| | - Matías Jaureguiberry-Bravo
- Program of Physiology and Biophysics, ICBM, Faculty of Medicine, Universidad de Chile, Santiago CP8380453, Chile Biomedical Neuroscience Institute, BNI, Faculty of Medicine, Universidad de Chile, Santiago CP8380453, Chile
| | - Daniela A Salas
- Program of Physiology and Biophysics, ICBM, Faculty of Medicine, Universidad de Chile, Santiago CP8380453, Chile Biomedical Neuroscience Institute, BNI, Faculty of Medicine, Universidad de Chile, Santiago CP8380453, Chile
| | - Omar A Ramírez
- Program of Physiology and Biophysics, ICBM, Faculty of Medicine, Universidad de Chile, Santiago CP8380453, Chile Biomedical Neuroscience Institute, BNI, Faculty of Medicine, Universidad de Chile, Santiago CP8380453, Chile Program of Anatomy and Development, ICBM, Faculty of Medicine, Universidad de Chile, Santiago CP8380453, Chile
| | - Víctor H Cornejo
- Program of Physiology and Biophysics, ICBM, Faculty of Medicine, Universidad de Chile, Santiago CP8380453, Chile Biomedical Neuroscience Institute, BNI, Faculty of Medicine, Universidad de Chile, Santiago CP8380453, Chile
| | - Hsiangmin E Lu
- Department of Physiology, University of Maryland School of Medicine, Baltimore, MD 21201, USA Program in Molecular Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Thomas A Blanpied
- Department of Physiology, University of Maryland School of Medicine, Baltimore, MD 21201, USA Program in Neuroscience, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Andrés Couve
- Program of Physiology and Biophysics, ICBM, Faculty of Medicine, Universidad de Chile, Santiago CP8380453, Chile Biomedical Neuroscience Institute, BNI, Faculty of Medicine, Universidad de Chile, Santiago CP8380453, Chile
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26
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Drp1 Loss-of-function Reduces Cardiomyocyte Oxygen Dependence Protecting the Heart From Ischemia-reperfusion Injury. J Cardiovasc Pharmacol 2014; 63:477-87. [DOI: 10.1097/fjc.0000000000000071] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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27
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Rizk A, Paul G, Incardona P, Bugarski M, Mansouri M, Niemann A, Ziegler U, Berger P, Sbalzarini IF. Segmentation and quantification of subcellular structures in fluorescence microscopy images using Squassh. Nat Protoc 2014; 9:586-96. [DOI: 10.1038/nprot.2014.037] [Citation(s) in RCA: 173] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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28
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McDonald JH, Dunn KW. Statistical tests for measures of colocalization in biological microscopy. J Microsc 2013; 252:295-302. [PMID: 24117417 PMCID: PMC4428547 DOI: 10.1111/jmi.12093] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Accepted: 09/16/2013] [Indexed: 11/30/2022]
Abstract
Colocalization analysis is the most common technique used for quantitative analysis of fluorescence microscopy images. Several metrics have been developed for measuring the colocalization of two probes, including Pearson's correlation coefficient (PCC) and Manders' correlation coefficient (MCC). However, once measured, the meaning of these measurements can be unclear; interpreting PCC or MCC values requires the ability to evaluate the significance of a particular measurement, or the significance of the difference between two sets of measurements. In previous work, we showed how spatial autocorrelation confounds randomization techniques commonly used for statistical analysis of colocalization data. Here we use computer simulations of biological images to show that the Student's one-sample t-test can be used to test the significance of PCC or MCC measurements of colocalization, and the Student's two-sample t-test can be used to test the significance of the difference between measurements obtained under different experimental conditions.
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Affiliation(s)
- John H McDonald
- Department of Biological Sciences, University of Delaware, Newark, Delaware, U.S.A
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29
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Abstract
Fluorescence microscopy can be used to assess quantitatively the interaction between a ligand and its receptor, between two macromolecules, or between a macromolecule and a particular intracellular compartment by co-localization analysis. In general, this analysis involves tagging potential interacting partners with distinct fluorophores-by direct labeling of a small ligand, by expression of fluorescent cDNA constructs, by immunofluorescence labeling, or by some combination of these methods. Pairwise comparison of the fluorescence intensity of the two fluorophores at each pixel in a two channel digital image of the sample reveals regions where both are present. With appropriate protocols, the image data can be interpreted to indicate where the potential interacting partners are co-localized. Keeping in mind the limited resolution of the light microscope, co-localization is often used to support the claim that two molecules are interacting.All quantitative methods for evaluating co-localization begin with identifying the pixels where the intensities of both color channels are above background. Typically this involves two sequential image segmentation steps: the first to exclude pixels where neither channel is above background, and the second to set overlap thresholds that exclude pixels where only one color channel is present. Following segmentation, various quantitative measures can be computed to describe the remaining subset of pixels where the two color channels overlap. These metrics range from simple calculation of the fraction of pixels where overlap occurs to more sophisticated image correlation metrics. Additional constraints may be employed to distinguish true co-localization from random overlap. Finally, an image map showing only the co-localized pixels may be displayed as an additional image channel in order to visualize the spatial distribution of co-localized pixels. Several commercial and open source software solutions provide this type of co-localization analysis, making image segmentation and calculation of metrics relatively straightforward. As an example, we provide a protocol for the time-dependent co-localization of fluorescently tagged lipoproteins with LDL receptor (LDLR) and with the early endosome marker EEA1.
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30
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Leiva N, Capmany A, Damiani MT. Rab11-family of interacting protein 2 associates with chlamydial inclusions through its Rab-binding domain and promotes bacterial multiplication. Cell Microbiol 2012; 15:114-29. [PMID: 23006599 DOI: 10.1111/cmi.12035] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Revised: 09/17/2012] [Accepted: 09/18/2012] [Indexed: 01/16/2023]
Abstract
Chlamydia trachomatis, an obligate intracellular pathogen, survives within host cells in a special compartment named 'inclusion' and takes advantage of host vesicular transport pathways for its growth and replication. Rab GTPases are key regulatory proteins of intracellular trafficking. Several Rabs, among them Rab11 and Rab14, are implicated in chlamydial development. FIP2, a member of the Rab11-Family of Interacting Proteins, presents at the C-terminus a Rab-binding domain that interacts with both Rab11 and Rab14. In this study, we determined and characterized the recruitment of endogenous and GFP-tagged FIP2 to the chlamydial inclusions. The recruitment of FIP2 is specific since other members of the Rab11-Family of Interacting Proteins do not associate with the chlamydial inclusions. The Rab-binding domain of FIP2 is essential for its association. Our results indicate that FIP2 binds to Rab11 at the chlamydial inclusion membrane through its Rab-binding domain. The presence of FIP2 at the chlamydial inclusion favours the recruitment of Rab14. Furthermore, our results show that FIP2 promotes inclusion development and bacterial replication. In agreement, the silencing of FIP2 decreases the bacterial progeny. C. trachomatis likely recruits FIP2 to hijack host intracellular trafficking to redirect vesicles full of nutrients towards the inclusion.
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Affiliation(s)
- Natalia Leiva
- Laboratory of Phagocytosis and Intracellular Trafficking, IHEM-CONICET, School of Medicine, University of Cuyo, Mendoza, Argentina
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Astorga G, Härtel S, Sanhueza M, Bacigalupo J. TRP, TRPL and cacophony channels mediate Ca2+ influx and exocytosis in photoreceptors axons in Drosophila. PLoS One 2012; 7:e44182. [PMID: 22952921 PMCID: PMC3432082 DOI: 10.1371/journal.pone.0044182] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2012] [Accepted: 08/02/2012] [Indexed: 01/17/2023] Open
Abstract
In Drosophila photoreceptors Ca(2+)-permeable channels TRP and TRPL are the targets of phototransduction, occurring in photosensitive microvilli and mediated by a phospholipase C (PLC) pathway. Using a novel Drosophila brain slice preparation, we studied the distribution and physiological properties of TRP and TRPL in the lamina of the visual system. Immunohistochemical images revealed considerable expression in photoreceptors axons at the lamina. Other phototransduction proteins are also present, mainly PLC and protein kinase C, while rhodopsin is absent. The voltage-dependent Ca(2+) channel cacophony is also present there. Measurements in the lamina with the Ca(2+) fluorescent protein G-CaMP ectopically expressed in photoreceptors, revealed depolarization-induced Ca(2+) increments mediated by cacophony. Additional Ca(2+) influx depends on TRP and TRPL, apparently functioning as store-operated channels. Single synaptic boutons resolved in the lamina by FM4-64 fluorescence revealed that vesicle exocytosis depends on cacophony, TRP and TRPL. In the PLC mutant norpA bouton labeling was also impaired, implicating an additional modulation by this enzyme. Internal Ca(2+) also contributes to exocytosis, since this process was reduced after Ca(2+)-store depletion. Therefore, several Ca(2+) pathways participate in photoreceptor neurotransmitter release: one is activated by depolarization and involves cacophony; this is complemented by internal Ca(2+) release and the activation of TRP and TRPL coupled to Ca(2+) depletion of internal reservoirs. PLC may regulate the last two processes. TRP and TRPL would participate in two different functions in distant cellular regions, where they are opened by different mechanisms. This work sheds new light on the mechanism of neurotransmitter release in tonic synapses of non-spiking neurons.
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Affiliation(s)
- Guadalupe Astorga
- Department of Biology, Faculty of Sciences, University of Chile, Santiago, Chile
- Millennium Institute for Cell Dynamics and Biotechnology, Faculty of Sciences, University of Chile, Santiago, Chile
| | - Steffen Härtel
- Laboratory for Scientific Image Analysis, (SCIAN-Lab), Biomedical Neuroscience Institute (BNI), ICBM, Program of Anatomy and Developmental Biology, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Magdalena Sanhueza
- Department of Biology, Faculty of Sciences, University of Chile, Santiago, Chile
- Millennium Institute for Cell Dynamics and Biotechnology, Faculty of Sciences, University of Chile, Santiago, Chile
| | - Juan Bacigalupo
- Department of Biology, Faculty of Sciences, University of Chile, Santiago, Chile
- Millennium Institute for Cell Dynamics and Biotechnology, Faculty of Sciences, University of Chile, Santiago, Chile
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Valdés V, Valenzuela JI, Salas DA, Jaureguiberry-Bravo M, Otero C, Thiede C, Schmidt CF, Couve A. Endoplasmic reticulum sorting and kinesin-1 command the targeting of axonal GABAB receptors. PLoS One 2012; 7:e44168. [PMID: 22952914 PMCID: PMC3428321 DOI: 10.1371/journal.pone.0044168] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Accepted: 07/30/2012] [Indexed: 12/17/2022] Open
Abstract
In neuronal cells the intracellular trafficking machinery controls the availability of neurotransmitter receptors at the plasma membrane, which is a critical determinant of synaptic strength. Metabotropic γ amino-butyric acid (GABA) type B receptors (GABABRs) are neurotransmitter receptors that modulate synaptic transmission by mediating the slow and prolonged responses to GABA. GABABRs are obligatory heteromers constituted by two subunits, GABABR1 and GABABR2. GABABR1a and GABABR1b are the most abundant subunit variants. GABABR1b is located in the somatodendritic domain whereas GABABR1a is additionally targeted to the axon. Sushi domains located at the N-terminus of GABABR1a constitute the only difference between both variants and are necessary and sufficient for axonal targeting. The precise targeting machinery and the organelles involved in sorting and transport have not been described. Here we demonstrate that GABABRs require the Golgi apparatus for plasma membrane delivery but that axonal sorting and targeting of GABABR1a operate in a pre-Golgi compartment. In the axon GABABR1a subunits are enriched in the endoplasmic reticulum (ER), and their dynamic behavior and colocalization with other secretory organelles like the ER-to-Golgi intermediate compartment (ERGIC) suggest that they employ a local secretory route. The transport of axonal GABABR1a is microtubule-dependent and kinesin-1, a molecular motor of the kinesin family, determines axonal localization. Considering that progression of GABABRs through the secretory pathway is regulated by an ER retention motif our data contribute to understand the role of the axonal ER in non-canonical sorting and targeting of neurotransmitter receptors.
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Affiliation(s)
- Viviana Valdés
- Biomedical Neuroscience Institute (BNI), Faculty of Medicine, Universidad de Chile, Santiago, Chile
- Program of Physiology and Biophysics, Institute of Biomedical Sciences (ICBM), Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - José Ignacio Valenzuela
- Biomedical Neuroscience Institute (BNI), Faculty of Medicine, Universidad de Chile, Santiago, Chile
- Program of Physiology and Biophysics, Institute of Biomedical Sciences (ICBM), Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Daniela A. Salas
- Biomedical Neuroscience Institute (BNI), Faculty of Medicine, Universidad de Chile, Santiago, Chile
- Program of Physiology and Biophysics, Institute of Biomedical Sciences (ICBM), Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Matías Jaureguiberry-Bravo
- Biomedical Neuroscience Institute (BNI), Faculty of Medicine, Universidad de Chile, Santiago, Chile
- Program of Physiology and Biophysics, Institute of Biomedical Sciences (ICBM), Faculty of Medicine, Universidad de Chile, Santiago, Chile
- School of Biochemistry, Faculty of Biological Science, Universidad Andrés Bello, Santiago, Chile
| | - Carolina Otero
- Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Christina Thiede
- Georg-August-Universität, Fakultät für Physik, Drittes Physikalisches Institut-Biophysik, Göttingen, Germany
| | - Christoph F. Schmidt
- Georg-August-Universität, Fakultät für Physik, Drittes Physikalisches Institut-Biophysik, Göttingen, Germany
| | - Andrés Couve
- Biomedical Neuroscience Institute (BNI), Faculty of Medicine, Universidad de Chile, Santiago, Chile
- Program of Physiology and Biophysics, Institute of Biomedical Sciences (ICBM), Faculty of Medicine, Universidad de Chile, Santiago, Chile
- * E-mail:
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Dudu V, Rotari V, Vazquez M. Sendai virus-based liposomes enable targeted cytosolic delivery of nanoparticles in brain tumor-derived cells. J Nanobiotechnology 2012; 10:9. [PMID: 22339792 PMCID: PMC3352066 DOI: 10.1186/1477-3155-10-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2011] [Accepted: 02/17/2012] [Indexed: 12/16/2022] Open
Abstract
Background Nanotechnology-based bioassays that detect the presence and/or absence of a combination of cell markers are increasingly used to identify stem or progenitor cells, assess cell heterogeneity, and evaluate tumor malignancy and/or chemoresistance. Delivery methods that enable nanoparticles to rapidly detect emerging, intracellular markers within cell clusters of biopsies will greatly aid in tumor characterization, analysis of functional state and development of treatment regimens. Results Experiments utilized the Sendai virus to achieve in vitro, cytosolic delivery of Quantum dots in cells cultured from Human brain tumors. Using fluorescence microscopy and Transmission Electron Microscopy, in vitro experiments illustrated that these virus-based liposomes decreased the amount of non-specifically endocytosed nanoparticles by 50% in the Human glioblastoma and medulloblastoma samples studied. Significantly, virus-based liposome delivery also facilitated targeted binding of Quantum dots to cytosolic Epidermal Growth Factor Receptor within cultured cells, focal to the early detection and characterization of malignant brain tumors. Conclusions These findings are the first to utilize the Sendai virus to achieve cytosolic, targeted intracellular binding of Qdots within Human brain tumor cells. The results are significant to the continued applicability of nanoparticles used for the molecular labeling of cancer cells to determine tumor heterogeneity, grade, and chemotherapeutic resistivity.
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Affiliation(s)
- Veronica Dudu
- The City College of New York, Department of Biomedical Engineering, 160 Convent Avenue, New York, NY 10031, USA
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Focal adhesion protein abnormalities in myelodysplastic mesenchymal stromal cells. Exp Cell Res 2011; 317:2616-29. [DOI: 10.1016/j.yexcr.2011.08.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2011] [Revised: 08/07/2011] [Accepted: 08/09/2011] [Indexed: 11/21/2022]
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Prieto CP, Krause BJ, Quezada C, San Martin R, Sobrevia L, Casanello P. Hypoxia-reduced nitric oxide synthase activity is partially explained by higher arginase-2 activity and cellular redistribution in human umbilical vein endothelium. Placenta 2011; 32:932-40. [PMID: 21962305 DOI: 10.1016/j.placenta.2011.09.003] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2011] [Revised: 08/18/2011] [Accepted: 09/07/2011] [Indexed: 01/08/2023]
Abstract
Hypoxia relates with altered placental vasodilation, and in isolated endothelial cells, it reduces activity of the endothelial nitric oxide synthase (eNOS) and l-arginine transport. It has been reported that arginase-2 expression, an alternative pathway for l-arginine metabolism, is increased in adult endothelial cells exposed to hypoxia as well as in pre-eclamptic placentae. We studied in human umbilical vein endothelial cells (HUVEC) whether hypoxia-reduced NO synthesis results from increased arginase-mediated l-arginine metabolism and changes in subcellular localization of eNOS and arginase-2. In HUVEC exposed (24 h) to 5% (normoxia) or 2% (hypoxia) oxygen, l-arginine transport kinetics, arginase activity (urea assay), and NO synthase (NOS) activity (l-citrulline assay) were determined. Arginase-1, arginase-2 and eNOS expression were determined by RT-PCR and Western blot. Subcellular localization of arginase-2 and eNOS were studied using confocal microscopy and indirect immunofluorescence. Experiments were done in absence or presence of S-(2-boronoethyl)-l-cysteine-HCl (BEC, arginase inhibitor) or N(G)-nitro-l-arginine methyl ester (l-NAME). Hypoxia-induced reduction in eNOS activity was associated with a reduction in eNOS phosphorylation at Serine-1177 and increased phosphorylation at Threonine-495. This was paralleled with an induction in arginase-2 expression and activity, and decreased l-arginine transport. In hypoxia the arginase inhibition, restored NO synthesis and l-arginine transport, without changes in the eNOS post-translational modification status. Hypoxia increased arginase-2/eNOS colocalization, and eNOS redistribution to the cell periphery. Altogether these data reinforce the thought that eNOS cell location, post-translational modification and substrate availability are important mechanisms regulating eNOS activity. If these mechanisms occur in pregnancy diseases where feto-placental oxygen levels are reduced remains to be clarified.
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Affiliation(s)
- C P Prieto
- Perinatology Research Laboratory (PRL), Division of Obstetrics and Gynaecology, School of Medicine, Faculty of Medicine, Pontificia Universidad Católica de Chile, Marcoleta 391, Santiago, Chile
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Schlapp G, Scavone P, Zunino P, Härtel S. Development of 3D architecture of uropathogenic Proteus mirabilis batch culture biofilms-A quantitative confocal microscopy approach. J Microbiol Methods 2011; 87:234-40. [PMID: 21864585 DOI: 10.1016/j.mimet.2011.07.021] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2011] [Revised: 07/25/2011] [Accepted: 07/28/2011] [Indexed: 10/17/2022]
Abstract
This work studies the development of the 3D architecture of batch culture P. mirabilis biofilms on the basis of morpho-topological descriptors calculated from confocal laser scanning microscopy (CLSM) stacks with image processing routines. A precise architectonical understanding of biofilm organization on a morpho-topological level is necessary to understand emergent interactions with the environment and the appearance of functionally different progeny swarmer cells. P. mirabilis biofilms were grown on glass coverslips for seven days on LB broth and subjected to in situ immunofluorescence. Confocal image stacks were deconvolved prior to segmentation of regions of interest (ROI) that identify individual bacteria and extracellular material, followed by 3D reconstruction and calculation of different morpho-topological key descriptors. Results showed that P. mirabilis biofilm formation followed a five stage process: (i) reversible adhesion to the surface characterized by slow growth, presence of elongated bacteria, and absence of extracellular material, (ii) irreversible bacterial adhesion concomitant to decreasing elongation, and the beginning of extracellular polymer production, (iii) accelerated bacterial growth concomitant to continuously decreasing elongation and halting of extracellular polymer production, (iv) maturation of biofilm defined by maximum bacterial density, volume, minimum elongation, maximum extracellular material, and highest compaction, and (v) decreased bacterial density and extracellular material through detachment and dispersion. Swarmer cells do not play a role in P. mirabilis biofilm formation under the applied conditions. Our approach sets the basis for future studies of 3D biofilm architecture using dynamic in vivo models and different environmental conditions that assess clinical impacts of P. mirabilis biofilm.
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Affiliation(s)
- G Schlapp
- Department of Microbiology, Instituto de Investigaciones Biológicas Clemente Estable, Avda. Italia 3318, Montevideo, Uruguay
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Velasquez SM, Ricardi MM, Dorosz JG, Fernandez PV, Nadra AD, Pol-Fachin L, Egelund J, Gille S, Harholt J, Ciancia M, Verli H, Pauly M, Bacic A, Olsen CE, Ulvskov P, Petersen BL, Somerville C, Iusem ND, Estevez JM. O-glycosylated cell wall proteins are essential in root hair growth. Science 2011; 332:1401-3. [PMID: 21680836 DOI: 10.1126/science.1206657] [Citation(s) in RCA: 210] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Root hairs are single cells that develop by tip growth and are specialized in the absorption of nutrients. Their cell walls are composed of polysaccharides and hydroxyproline-rich glycoproteins (HRGPs) that include extensins (EXTs) and arabinogalactan-proteins (AGPs). Proline hydroxylation, an early posttranslational modification of HRGPs that is catalyzed by prolyl 4-hydroxylases (P4Hs), defines the subsequent O-glycosylation sites in EXTs (which are mainly arabinosylated) and AGPs (which are mainly arabinogalactosylated). We explored the biological function of P4Hs, arabinosyltransferases, and EXTs in root hair cell growth. Biochemical inhibition or genetic disruption resulted in the blockage of polarized growth in root hairs and reduced arabinosylation of EXTs. Our results demonstrate that correct O-glycosylation on EXTs is essential for cell-wall self-assembly and, hence, root hair elongation in Arabidopsis thaliana.
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Affiliation(s)
- Silvia M Velasquez
- Instituto de Fisiología, Biología Molecular y Neurociencias-Consejo Nacional de Investigaciones Científicas y Técnicas (IFIByNE-CONICET), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina
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Villalta JI, Galli S, Iacaruso MF, Antico Arciuch VG, Poderoso JJ, Jares-Erijman EA, Pietrasanta LI. New algorithm to determine true colocalization in combination with image restoration and time-lapse confocal microscopy to MAP kinases in mitochondria. PLoS One 2011; 6:e19031. [PMID: 21559502 PMCID: PMC3084741 DOI: 10.1371/journal.pone.0019031] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2010] [Accepted: 03/14/2011] [Indexed: 11/19/2022] Open
Abstract
The subcellular localization and physiological functions of biomolecules are closely related and thus it is crucial to precisely determine the distribution of different molecules inside the intracellular structures. This is frequently accomplished by fluorescence microscopy with well-characterized markers and posterior evaluation of the signal colocalization. Rigorous study of colocalization requires statistical analysis of the data, albeit yet no single technique has been established as a standard method. Indeed, the few methods currently available are only accurate in images with particular characteristics. Here, we introduce a new algorithm to automatically obtain the true colocalization between images that is suitable for a wide variety of biological situations. To proceed, the algorithm contemplates the individual contribution of each pixel's fluorescence intensity in a pair of images to the overall Pearsońs correlation and Manders' overlap coefficients. The accuracy and reliability of the algorithm was validated on both simulated and real images that reflected the characteristics of a range of biological samples. We used this algorithm in combination with image restoration by deconvolution and time-lapse confocal microscopy to address the localization of MEK1 in the mitochondria of different cell lines. Appraising the previously described behavior of Akt1 corroborated the reliability of the combined use of these techniques. Together, the present work provides a novel statistical approach to accurately and reliably determine the colocalization in a variety of biological images.
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Affiliation(s)
- Jorge Ignacio Villalta
- Centro de Microscopías Avanzadas, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Soledad Galli
- Departamento de Química Orgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, CIHIDECAR, CONICET, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - María Florencia Iacaruso
- Centro de Microscopías Avanzadas, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Valeria Gabriela Antico Arciuch
- Laboratory of Oxygen Metabolism, University Hospital “José de San Martín,” Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Juan José Poderoso
- Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
- Laboratory of Oxygen Metabolism, University Hospital “José de San Martín,” Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Elizabeth Andrea Jares-Erijman
- Departamento de Química Orgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, CIHIDECAR, CONICET, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Lía Isabel Pietrasanta
- Centro de Microscopías Avanzadas, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
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Dunn KW, Kamocka MM, McDonald JH. A practical guide to evaluating colocalization in biological microscopy. Am J Physiol Cell Physiol 2011; 300:C723-42. [PMID: 21209361 PMCID: PMC3074624 DOI: 10.1152/ajpcell.00462.2010] [Citation(s) in RCA: 1389] [Impact Index Per Article: 106.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2010] [Accepted: 01/02/2011] [Indexed: 11/22/2022]
Abstract
Fluorescence microscopy is one of the most powerful tools for elucidating the cellular functions of proteins and other molecules. In many cases, the function of a molecule can be inferred from its association with specific intracellular compartments or molecular complexes, which is typically determined by comparing the distribution of a fluorescently labeled version of the molecule with that of a second, complementarily labeled probe. Although arguably the most common application of fluorescence microscopy in biomedical research, studies evaluating the "colocalization" of two probes are seldom quantified, despite a diversity of image analysis tools that have been specifically developed for that purpose. Here we provide a guide to analyzing colocalization in cell biology studies, emphasizing practical application of quantitative tools that are now widely available in commercial and free image analysis software.
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Affiliation(s)
- Kenneth W Dunn
- Dept. of Medicine, Division of Nephrology, Indiana Univ. Medical Center, Indianapolis, IN 46202, USA.
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Kramer LB, Shim J, Previtera ML, Isack NR, Lee MC, Firestein BL, Rongo C. UEV-1 is an ubiquitin-conjugating enzyme variant that regulates glutamate receptor trafficking in C. elegans neurons. PLoS One 2010; 5:e14291. [PMID: 21179194 PMCID: PMC3001443 DOI: 10.1371/journal.pone.0014291] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2010] [Accepted: 11/18/2010] [Indexed: 11/18/2022] Open
Abstract
The regulation of AMPA-type glutamate receptor (AMPAR) membrane trafficking is a key mechanism by which neurons regulate synaptic strength and plasticity. AMPAR trafficking is modulated through a combination of receptor phosphorylation, ubiquitination, endocytosis, and recycling, yet the factors that mediate these processes are just beginning to be uncovered. Here we identify the ubiquitin-conjugating enzyme variant UEV-1 as a regulator of AMPAR trafficking in vivo. We identified mutations in uev-1 in a genetic screen for mutants with altered trafficking of the AMPAR subunit GLR-1 in C. elegans interneurons. Loss of uev-1 activity results in the accumulation of GLR-1 in elongated accretions in neuron cell bodies and along the ventral cord neurites. Mutants also have a corresponding behavioral defect--a decrease in spontaneous reversals in locomotion--consistent with diminished GLR-1 function. The localization of other synaptic proteins in uev-1-mutant interneurons appears normal, indicating that the GLR-1 trafficking defects are not due to gross deficiencies in synapse formation or overall protein trafficking. We provide evidence that GLR-1 accumulates at RAB-10-containing endosomes in uev-1 mutants, and that receptors arrive at these endosomes independent of clathrin-mediated endocytosis. UEV-1 homologs in other species bind to the ubiquitin-conjugating enzyme Ubc13 to create K63-linked polyubiquitin chains on substrate proteins. We find that whereas UEV-1 can interact with C. elegans UBC-13, global levels of K63-linked ubiquitination throughout nematodes appear to be unaffected in uev-1 mutants, even though UEV-1 is broadly expressed in most tissues. Nevertheless, ubc-13 mutants are similar in phenotype to uev-1 mutants, suggesting that the two proteins do work together to regulate GLR-1 trafficking. Our results suggest that UEV-1 could regulate a small subset of K63-linked ubiquitination events in nematodes, at least one of which is critical in regulating GLR-1 trafficking.
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Affiliation(s)
- Lawrence B Kramer
- The Waksman Institute, Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, New Jersey, United States of America
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