1701
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Leithner A, Renkawitz J, De Vries I, Hauschild R, Häcker H, Sixt M. Fast and efficient genetic engineering of hematopoietic precursor cells for the study of dendritic cell migration. Eur J Immunol 2018; 48:1074-1077. [PMID: 29436709 DOI: 10.1002/eji.201747358] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 01/03/2018] [Accepted: 02/01/2018] [Indexed: 12/29/2022]
Abstract
Estrogen inducible Hoxb8 leads to conditional immortalization of hematopoietic precursors. These cells can be cultured and infected with the CRISPR/Cas9 system for genome editing, circumventing resource consuming generation of mouse models. The resultant cells retain their ability to differentiate into migratory dendritic cells.
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Affiliation(s)
- Alexander Leithner
- Institute of Science and Technology Austria, Am Campus 1, Klosterneuburg, Austria
| | - Joerg Renkawitz
- Institute of Science and Technology Austria, Am Campus 1, Klosterneuburg, Austria
| | - Ingrid De Vries
- Institute of Science and Technology Austria, Am Campus 1, Klosterneuburg, Austria
| | - Robert Hauschild
- Institute of Science and Technology Austria, Am Campus 1, Klosterneuburg, Austria
| | - Hans Häcker
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Michael Sixt
- Institute of Science and Technology Austria, Am Campus 1, Klosterneuburg, Austria
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1702
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Allier C, Vincent R, Navarro F, Menneteau M, Ghenim L, Gidrol X, Bordy T, Hervé L, Cioni O, Bardin S, Bornens M, Usson Y, Morales S. Lens-free Video Microscopy for the Dynamic and Quantitative Analysis of Adherent Cell Culture. J Vis Exp 2018. [PMID: 29553497 DOI: 10.3791/56580] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Here, we demonstrate that lens-free video microscopy enables us to simultaneously capture the kinetics of thousands of cells directly inside the incubator and that it is possible to monitor and quantify single cells along several cell cycles. We describe the full protocol used to monitor and quantify a HeLa cell culture for 2.7 days. First, cell culture acquisition is performed with a lens-free video microscope, and then the data is analyzed following a four-step process: multi-wavelength holographic reconstruction, cell-tracking, cell segmentation and cell division detection algorithms. As a result, we show that it is possible to gather a dataset featuring more than 10,000 cell cycle tracks and more than 2 x 106 cell morphological measurements.
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Affiliation(s)
| | | | | | | | - Lamya Ghenim
- CEA, INSERM, BIG, Université Grenoble Alpes; CNRS, FR CNRS 3425
| | | | - Thomas Bordy
- CEA, LETI, DTBS, LISA, Université Grenoble Alpes
| | - Lionel Hervé
- CEA, LETI, DTBS, LISA, Université Grenoble Alpes
| | | | - Sabine Bardin
- CNRS, UMR 144, Molecular Mechanisms of Intracellular Transport, PSL Research University, Institut Curie
| | - Michel Bornens
- CNRS, UMR 144, Molecular Mechanisms of Intracellular Transport, PSL Research University, Institut Curie
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1703
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O'Neal L, Mukherjee T, Alexandre G. Analyzing Chemotaxis and Related Behaviors of Azospirillum Brasilense. ACTA ACUST UNITED AC 2018; 48:3E.3.1-3E.3.11. [PMID: 29512118 DOI: 10.1002/cpmc.49] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Bacteria of the genus A. brasilense are motile and capable of chemotaxis and aerotaxis (taxis in gradient of oxygen) using a single polar flagellum that propels the cells in aqueous environments. Responses to attractants and repellents have been described and spatial gradient assays that permit the visualization of these responses are detailed in this unit. These assays are simple and can be readily implemented with minimum set ups. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Lindsey O'Neal
- Biochemistry &Cellular and Molecular Biology, The University of Tennessee, Knoxville, Tennesee
| | - Tanmoy Mukherjee
- Biochemistry &Cellular and Molecular Biology, The University of Tennessee, Knoxville, Tennesee
| | - Gladys Alexandre
- Biochemistry &Cellular and Molecular Biology, The University of Tennessee, Knoxville, Tennesee
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1704
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Hussain S, Wivagg CN, Szwedziak P, Wong F, Schaefer K, Izoré T, Renner LD, Holmes MJ, Sun Y, Bisson-Filho AW, Walker S, Amir A, Löwe J, Garner EC. MreB filaments align along greatest principal membrane curvature to orient cell wall synthesis. eLife 2018; 7:32471. [PMID: 29469806 PMCID: PMC5854468 DOI: 10.7554/elife.32471] [Citation(s) in RCA: 120] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 02/21/2018] [Indexed: 12/26/2022] Open
Abstract
MreB is essential for rod shape in many bacteria. Membrane-associated MreB filaments move around the rod circumference, helping to insert cell wall in the radial direction to reinforce rod shape. To understand how oriented MreB motion arises, we altered the shape of Bacillus subtilis. MreB motion is isotropic in round cells, and orientation is restored when rod shape is externally imposed. Stationary filaments orient within protoplasts, and purified MreB tubulates liposomes in vitro, orienting within tubes. Together, this demonstrates MreB orients along the greatest principal membrane curvature, a conclusion supported with biophysical modeling. We observed that spherical cells regenerate into rods in a local, self-reinforcing manner: rapidly propagating rods emerge from small bulges, exhibiting oriented MreB motion. We propose that the coupling of MreB filament alignment to shape-reinforcing peptidoglycan synthesis creates a locally-acting, self-organizing mechanism allowing the rapid establishment and stable maintenance of emergent rod shape. Many bacteria are surrounded by both a cell membrane and a cell wall – a rigid outer covering made of sugars and short protein chains. The cell wall often determines which of a variety of shapes – such as rods or spheres – the bacteria grow into. One protein required to form the rod shape is called MreB. This protein forms filaments that bind to the bacteria’s cell membrane and associate with the enzymes that build the cell wall. Together, these filament-enzyme complexes rotate around the cell to build and reinforce the cell wall in a hoop-like manner. But how do the MreB filaments know how to move around the circumference of the rod, instead of moving in any other direction? Using a technique called total internal reflection microscopy to study how MreB filaments move across bacteria cells, Hussain, Wivagg et al. show that the filaments sense the shape of a bacterium by orienting along the direction of greatest curvature. As a result, the filaments in rod-shaped cells orient and move around the rod, while in spherical bacteria they move in all directions. However, spherical bacteria can regenerate into rods from small surface ‘bulges’. The MreB filaments in the bulges move in an oriented way, helping them to generate the rod shape. Hussain, Wivagg et al. also found that forcing cells that lack a cell wall into a rod shape caused the MreB filaments bound to the cell membrane to orient and circle around the rod. This shows that the organization of the filaments is sufficient to shape the cell wall. In the future, determining what factors control the activity of the MreB filaments and the enzymes they associate with might reveal new targets for antibiotics that disrupt the cell wall and so kill the bacteria. This will require higher resolution microscopes to be used to examine the cell wall in more detail. The activity of all the proteins involved in building cell walls will also need to be extensively characterized.
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Affiliation(s)
- Saman Hussain
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - Carl N Wivagg
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - Piotr Szwedziak
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Felix Wong
- Harvard John A. Paulson School of Engineering and Applied Sciences, Cambridge, United States
| | - Kaitlin Schaefer
- Department of Microbiology and Immunology, Harvard University, Cambridge, United States
| | - Thierry Izoré
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Lars D Renner
- Leibniz Institute of Polymer Research, Dresden, Germany
| | - Matthew J Holmes
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - Yingjie Sun
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | | | - Suzanne Walker
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, United States
| | - Ariel Amir
- Harvard John A. Paulson School of Engineering and Applied Sciences, Cambridge, United States
| | - Jan Löwe
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Ethan C Garner
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
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1705
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Roque H, Saurya S, Pratt MB, Johnson E, Raff JW. Drosophila PLP assembles pericentriolar clouds that promote centriole stability, cohesion and MT nucleation. PLoS Genet 2018; 14:e1007198. [PMID: 29425198 PMCID: PMC5823460 DOI: 10.1371/journal.pgen.1007198] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Revised: 02/22/2018] [Accepted: 01/12/2018] [Indexed: 12/31/2022] Open
Abstract
Pericentrin is a conserved centrosomal protein whose dysfunction has been linked to several human diseases. It has been implicated in many aspects of centrosome and cilia function, but its precise role is unclear. Here, we examine Drosophila Pericentrin-like-protein (PLP) function in vivo in tissues that form both centrosomes and cilia. Plp mutant centrioles exhibit four major defects: (1) They are short and have subtle structural abnormalities; (2) They disengage prematurely, and so overduplicate; (3) They organise fewer cytoplasmic MTs during interphase; (4) When forming cilia, they fail to establish and/or maintain a proper connection to the plasma membrane—although, surprisingly, they can still form an axoneme-like structure that can recruit transition zone (TZ) proteins. We show that PLP helps assemble “pericentriolar clouds” of electron-dense material that emanate from the central cartwheel spokes and spread outward to surround the mother centriole. We propose that the partial loss of these structures may largely explain the complex centriole, centrosome and cilium defects we observe in Plp mutant cells. Centrioles are complex, microtubule (MT) based structures that organise two important cell organelles, the centrosome and the cilium. The centrosome is a major MT organising centre in many cell types, while the cilium functions as a cellular “antenna” responsible for regulating several cellular signalling pathways. Pericentrin is conserved centriole-binding protein that plays an important part in centrosome and cilium function, and mutations in the Pericentrin gene are linked to several human diseases. Here we use the fruit-fly Drosophila melanogaster to investigate how Pericentrin-Like-Protein (the fly homolog of Pericentrin) contributes to centriole, centrosome and cilium function. We find that Plp mutant fly centrioles have subtle structural defects, organize less microtubules, and do not properly migrate to the cell membrane to form cilia. We also observe that PLP helps assemble “pericentriolar clouds”—dense structures that emanate from the centriole, and appear to interact with microtubules, as well as connect existing centrioles to newly formed ones. In mutant flies these structures are significantly reduced in size. We propose that the defects in these PLP structures can explain most, if not all, the complex defects observed in Plp mutants.
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Affiliation(s)
- Helio Roque
- The Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, United Kingdom
| | - Saroj Saurya
- The Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, United Kingdom
| | - Metta B. Pratt
- The Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, United Kingdom
| | - Errin Johnson
- The Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, United Kingdom
| | - Jordan W. Raff
- The Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, United Kingdom
- * E-mail:
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1706
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Zhou X, Franklin RA, Adler M, Jacox JB, Bailis W, Shyer JA, Flavell RA, Mayo A, Alon U, Medzhitov R. Circuit Design Features of a Stable Two-Cell System. Cell 2018; 172:744-757.e17. [PMID: 29398113 PMCID: PMC7377352 DOI: 10.1016/j.cell.2018.01.015] [Citation(s) in RCA: 245] [Impact Index Per Article: 40.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 11/06/2017] [Accepted: 01/08/2018] [Indexed: 12/14/2022]
Abstract
Cell communication within tissues is mediated by multiple paracrine signals including growth factors, which control cell survival and proliferation. Cells and the growth factors they produce and receive constitute a circuit with specific properties that ensure homeostasis. Here, we used computational and experimental approaches to characterize the features of cell circuits based on growth factor exchange between macrophages and fibroblasts, two cell types found in most mammalian tissues. We found that the macrophage-fibroblast cell circuit is stable and robust to perturbations. Analytical screening of all possible two-cell circuit topologies revealed the circuit features sufficient for stability, including environmental constraint and negative-feedback regulation. Moreover, we found that cell-cell contact is essential for the stability of the macrophage-fibroblast circuit. These findings illustrate principles of cell circuit design and provide a quantitative perspective on cell interactions.
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Affiliation(s)
- Xu Zhou
- Howard Hughes Medical Institute, Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Ruth A Franklin
- Howard Hughes Medical Institute, Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Miri Adler
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Jeremy B Jacox
- Howard Hughes Medical Institute, Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA; Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Will Bailis
- Howard Hughes Medical Institute, Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Justin A Shyer
- Howard Hughes Medical Institute, Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Richard A Flavell
- Howard Hughes Medical Institute, Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Avi Mayo
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Uri Alon
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, 7610001, Israel.
| | - Ruslan Medzhitov
- Howard Hughes Medical Institute, Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA.
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1707
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Handberg-Thorsager M, Gutierrez-Mazariegos J, Arold ST, Kumar Nadendla E, Bertucci PY, Germain P, Tomançak P, Pierzchalski K, Jones JW, Albalat R, Kane MA, Bourguet W, Laudet V, Arendt D, Schubert M. The ancestral retinoic acid receptor was a low-affinity sensor triggering neuronal differentiation. SCIENCE ADVANCES 2018; 4:eaao1261. [PMID: 29492455 PMCID: PMC5821490 DOI: 10.1126/sciadv.aao1261] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 01/10/2018] [Indexed: 06/02/2023]
Abstract
Retinoic acid (RA) is an important intercellular signaling molecule in vertebrate development, with a well-established role in the regulation of hox genes during hindbrain patterning and in neurogenesis. However, the evolutionary origin of the RA signaling pathway remains elusive. To elucidate the evolution of the RA signaling system, we characterized RA metabolism and signaling in the marine annelid Platynereis dumerilii, a powerful model for evolution, development, and neurobiology. Binding assays and crystal structure analyses show that the annelid retinoic acid receptor (RAR) binds RA and activates transcription just as vertebrate RARs, yet with a different ligand-binding pocket and lower binding affinity, suggesting a permissive rather than instructive role of RA signaling. RAR knockdown and RA treatment of swimming annelid larvae further reveal that the RA signal is locally received in the medial neuroectoderm, where it controls neurogenesis and axon outgrowth, whereas the spatial colinear hox gene expression in the neuroectoderm remains unaffected. These findings suggest that one early role of the new RAR in bilaterian evolution was to control the spatially restricted onset of motor and interneuron differentiation in the developing ventral nerve cord and to indicate that the regulation of hox-controlled anterior-posterior patterning arose only at the base of the chordates, concomitant with a high-affinity RAR needed for the interpretation of a complex RA gradient.
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Affiliation(s)
- Mette Handberg-Thorsager
- Developmental Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69012 Heidelberg, Germany
| | - Juliana Gutierrez-Mazariegos
- Molecular Zoology Team, Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Lyon 1, CNRS, Institut National de la Recherche Agronomique, Ecole Normale Supérieure de Lyon, 46 Allée d’Italie, 69364 Lyon Cedex 07, France
| | - Stefan T. Arold
- King Abdullah University of Science and Technology, Center for Computational Bioscience Research, Division of Biological and Environmental Sciences and Engineering, Thuwal 23955-6900, Saudi Arabia
| | - Eswar Kumar Nadendla
- Centre de Biochimie Structurale, Inserm, CNRS, Université de Montpellier, 29 Rue de Navacelles, 34090 Montpellier, France
| | - Paola Y. Bertucci
- Developmental Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69012 Heidelberg, Germany
| | - Pierre Germain
- Centre de Biochimie Structurale, Inserm, CNRS, Université de Montpellier, 29 Rue de Navacelles, 34090 Montpellier, France
| | - Pavel Tomançak
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Keely Pierzchalski
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 North Pine Street, Baltimore, MD 21201, USA
| | - Jace W. Jones
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 North Pine Street, Baltimore, MD 21201, USA
| | - Ricard Albalat
- Departament de Genètica, Microbiologia i Estadística, Institut de Recerca de la Biodiversitat (IRBio), Facultat de Biologia, Universitat de Barcelona, Avinguda Diagonal 643, 08028 Barcelona, Spain
| | - Maureen A. Kane
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 North Pine Street, Baltimore, MD 21201, USA
| | - William Bourguet
- Centre de Biochimie Structurale, Inserm, CNRS, Université de Montpellier, 29 Rue de Navacelles, 34090 Montpellier, France
| | - Vincent Laudet
- Molecular Zoology Team, Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Lyon 1, CNRS, Institut National de la Recherche Agronomique, Ecole Normale Supérieure de Lyon, 46 Allée d’Italie, 69364 Lyon Cedex 07, France
| | - Detlev Arendt
- Developmental Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69012 Heidelberg, Germany
- Centre for Organismal Studies, University of Heidelberg, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
| | - Michael Schubert
- Sorbonne Universités, Université Pierre et Marie Curie (UPMC) Université Paris 06, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Observatoire Océanologique de Villefranche-sur-Mer, 181 Chemin du Lazaret, 06230 Villefranche-sur-Mer, France
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1708
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Cavicchi RE, King J, Ripple DC. Measurement of Average Aggregate Density by Sedimentation and Brownian Motion Analysis. J Pharm Sci 2018; 107:1304-1312. [PMID: 29409841 DOI: 10.1016/j.xphs.2018.01.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 01/09/2018] [Accepted: 01/10/2018] [Indexed: 12/21/2022]
Abstract
The spatially averaged density of protein aggregates is an important parameter that can be used to relate size distributions measured by orthogonal methods, to characterize protein particles, and perhaps to estimate the amount of protein in aggregate form in a sample. We obtained a series of images of protein aggregates exhibiting Brownian diffusion while settling under the influence of gravity in a sealed capillary. The aggregates were formed by stir-stressing a monoclonal antibody (NISTmAb). Image processing yielded particle tracks, which were then examined to determine settling velocity and hydrodynamic diameter down to 1 μm based on mean square displacement analysis. Measurements on polystyrene calibration microspheres ranging in size from 1 to 5 μm showed that the mean square displacement diameter had improved accuracy over the diameter derived from imaged particle area, suggesting a future method for correcting size distributions based on imaging. Stokes' law was used to estimate the density of each particle. It was found that the aggregates were highly porous with density decreasing from 1.080 to 1.028 g/cm3 as the size increased from 1.37 to 4.9 μm.
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Affiliation(s)
- Richard E Cavicchi
- Bioprocess Measurements Group, National Institute of Standards and Technology, Gaithersburg, Maryland 20899.
| | - Jason King
- Bioprocess Measurements Group, National Institute of Standards and Technology, Gaithersburg, Maryland 20899; XSOLIS, Nashville, Tennessee 37217
| | - Dean C Ripple
- Bioprocess Measurements Group, National Institute of Standards and Technology, Gaithersburg, Maryland 20899
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1709
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Rhinoscleroma pathogenesis: The type K3 capsule of Klebsiella rhinoscleromatis is a virulence factor not involved in Mikulicz cells formation. PLoS Negl Trop Dis 2018; 12:e0006201. [PMID: 29381692 PMCID: PMC5806929 DOI: 10.1371/journal.pntd.0006201] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 02/09/2018] [Accepted: 12/31/2017] [Indexed: 12/16/2022] Open
Abstract
Rhinoscleroma is a human specific chronic granulomatous infection of the nose and upper airways caused by the Gram-negative bacterium Klebsiella pneumoniae subsp. rhinoscleromatis. Although considered a rare disease, it is endemic in low-income countries where hygienic conditions are poor. A hallmark of this pathology is the appearance of atypical foamy monocytes called Mikulicz cells. However, the pathogenesis of rhinoscleroma remains poorly investigated. Capsule polysaccharide (CPS) is a prominent virulence factor in bacteria. All K. rhinoscleromatis strains are of K3 serotype, suggesting that CPS can be an important driver of rhinoscleroma disease. In this study, we describe the creation of the first mutant of K. rhinoscleromatis, inactivated in its capsule export machinery. Using a murine model recapitulating the formation of Mikulicz cells in lungs, we observed that a K. rhinoscleromatis CPS mutant (KR cps-) is strongly attenuated and that mice infected with a high dose of KR cps- are still able to induce Mikulicz cells formation, unlike a K. pneumoniae capsule mutant, and to partially recapitulate the characteristic strong production of IL-10. Altogether, the results of this study show that CPS is a virulence factor of K. rhinoscleromatis not involved in the specific appearance of Mikulicz cells.
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1710
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van Gisbergen PAC, Wu SZ, Chang M, Pattavina KA, Bartlett ME, Bezanilla M. An ancient Sec10-formin fusion provides insights into actin-mediated regulation of exocytosis. J Cell Biol 2018; 217:945-957. [PMID: 29374070 PMCID: PMC5839782 DOI: 10.1083/jcb.201705084] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 12/21/2017] [Accepted: 01/08/2018] [Indexed: 11/22/2022] Open
Abstract
Interactions between actin nucleators and the exocyst in yeast and mammals control membrane remodeling. van Gisbergen et al. now describe For1F, a fusion of an exocyst subunit (Sec10) and an actin nucleation factor (formin), retained in the moss lineage for more than 170 million years, which provides unique insight into the regulation of exocytosis by actin. Exocytosis, facilitated by the exocyst, is fundamentally important for remodeling cell walls and membranes. Here, we analyzed For1F, a novel gene that encodes a fusion of an exocyst subunit (Sec10) and an actin nucleation factor (formin). We showed that the fusion occurred early in moss evolution and has been retained for more than 170 million years. In Physcomitrella patens, For1F is essential, and the expressed protein is a fusion of Sec10 and formin. Reduction of For1F or actin filaments inhibits exocytosis, and For1F dynamically associates with Sec6, another exocyst subunit, in an actin-dependent manner. Complementation experiments demonstrate that constitutive expression of either half of the gene or the paralogous Sec10b rescues loss of For1F, suggesting that fusion of the two domains is not essential, consistent with findings in yeast, where formin and the exocyst are linked noncovalently. Although not essential, the fusion may have had selective advantages and provides a unique opportunity to probe actin regulation of exocytosis.
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Affiliation(s)
| | - Shu-Zon Wu
- Biological Sciences Department, Dartmouth College, Hanover, NH
| | - Mingqin Chang
- Biological Sciences Department, Dartmouth College, Hanover, NH.,Plant Biology Graduate Program, University of Massachusetts Amherst, Amherst, MA
| | - Kelli A Pattavina
- Molecular and Cellular Biology Graduate Program, University of Massachusetts Amherst, Amherst, MA
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1711
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Laird CT, Hassanein W, O'Neill NA, French BM, Cheng X, Fogler WE, Magnani JL, Parsell D, Cimeno A, Phelps CJ, Ayares D, Burdorf L, Azimzadeh AM, Pierson RN. P- and E-selectin receptor antagonism prevents human leukocyte adhesion to activated porcine endothelial monolayers and attenuates porcine endothelial damage. Xenotransplantation 2018; 25:e12381. [PMID: 29359469 DOI: 10.1111/xen.12381] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 11/24/2017] [Accepted: 01/02/2018] [Indexed: 01/05/2023]
Abstract
BACKGROUND Alongside the need to develop more effective and less toxic immunosuppression, the shortage of human organs available for organ transplantation is one of the major hurdles facing the field. Research into xenotransplantation, as an alternative source of organs, has unveiled formidable challenges. Porcine lungs perfused with human blood rapidly sequester the majority of circulating neutrophils and platelets, which leads to inflammation and organ failure within hours, and is not significantly attenuated by genetic modifications to the pig targeted to diminish antibody binding and complement and coagulation cascade activation. METHODS Here, we model the interaction of freshly isolated human leukocytes with xenotransplanted vasculature under physiologic flow conditions using microfluidic channels coated with porcine endothelial cells. Both isolated human neutrophils and whole human blood were perfused over transgenic pig aortic endothelial cells that had been activated with rhTNF-α or rhIL-4 using the BioFlux system. Novel compounds GMI-1271 and rPSGL1.Fc were tested as E- and P- selectin antagonists, respectively. Cellular adhesion and rolling events were tracked using FIJI (imageJ). RESULTS Porcine endothelium activated with either rhTNF-α or rhIL-4 expressed high amounts of selectins, to which isolated human neutrophils readily rolled and tethered. Both E-and P-selectin antagonism significantly reduced the number of neutrophils rolling and rolling distance in a dose-dependent manner, with near total inhibition at higher doses (P < .001). Similarly, with whole human blood, selectin blocking compounds exhibited dose-dependent inhibition of prevalent leukocyte adhesion and severe endothelial injury (Untreated: 394 ± 97 PMNs/hpf, 57 ± 6% loss EC; GMI1271+rPSGL1.Fc: 23 ± 9 PMNs/hpf, 8 ± 6% loss EC P < .01). CONCLUSIONS Selectin blockade may be useful as part of an integrated strategy to prevent neutrophil-mediated organ xenograft injury, especially during the early time points following reperfusion.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Richard N Pierson
- University of Maryland SOM, Baltimore, MD, USA.,GlycoMimetics, Inc, Rockville, MD, USA
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1712
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Bademosi AT, Lauwers E, Amor R, Verstreken P, van Swinderen B, Meunier FA. In Vivo Single-Molecule Tracking at the Drosophila Presynaptic Motor Nerve Terminal. J Vis Exp 2018. [PMID: 29364242 PMCID: PMC5908646 DOI: 10.3791/56952] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
An increasing number of super-resolution microscopy techniques are helping to uncover the mechanisms that govern the nanoscale cellular world. Single-molecule imaging is gaining momentum as it provides exceptional access to the visualization of individual molecules in living cells. Here, we describe a technique that we developed to perform single-particle tracking photo-activated localization microscopy (sptPALM) in Drosophila larvae. Synaptic communication relies on key presynaptic proteins that act by docking, priming, and promoting the fusion of neurotransmitter-containing vesicles with the plasma membrane. A range of protein-protein and protein-lipid interactions tightly regulates these processes and the presynaptic proteins therefore exhibit changes in mobility associated with each of these key events. Investigating how mobility of these proteins correlates with their physiological function in an intact live animal is essential to understanding their precise mechanism of action. Extracting protein mobility with high resolution in vivo requires overcoming limitations such as optical transparency, accessibility, and penetration depth. We describe how photoconvertible fluorescent proteins tagged to the presynaptic protein Syntaxin-1A can be visualized via slight oblique illumination and tracked at the motor nerve terminal or along the motor neuron axon of the third instar Drosophila larva.
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Affiliation(s)
- Adekunle T Bademosi
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland
| | - Elsa Lauwers
- VIB Centre for Brain and Disease Research, KU Leuven Department of Neurosciences, Leuven Institute for Neurodegenerative Disease (LIND)
| | - Rumelo Amor
- Queensland Brain Institute, The University of Queensland
| | - Patrik Verstreken
- VIB Centre for Brain and Disease Research, KU Leuven Department of Neurosciences, Leuven Institute for Neurodegenerative Disease (LIND)
| | | | - Frédéric A Meunier
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland;
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1713
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Lee BH, Park HY. HybTrack: A hybrid single particle tracking software using manual and automatic detection of dim signals. Sci Rep 2018; 8:212. [PMID: 29317715 PMCID: PMC5760724 DOI: 10.1038/s41598-017-18569-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 12/13/2017] [Indexed: 02/08/2023] Open
Abstract
Single particle tracking is a compelling technique for investigating the dynamics of nanoparticles and biological molecules in a broad range of research fields. In particular, recent advances in fluorescence microscopy have made single molecule tracking a prevalent method for studying biomolecules with a high spatial and temporal precision. Particle tracking algorithms have matured over the past three decades into more easily accessible platforms. However, there is an inherent difficulty in tracing particles that have a low signal-to-noise ratio and/or heterogeneous subpopulations. Here, we present a new MATLAB based tracking program which combines the benefits of manual and automatic tracking methods. The program prompts the user to manually locate a particle when an ambiguous situation occurs during automatic tracking. We demonstrate the utility of this program by tracking the movement of β-actin mRNA in the dendrites of cultured hippocampal neurons. We show that the diffusion coefficient of β-actin mRNA decreases upon neuronal stimulation by bicuculline treatment. This tracking method enables an efficient dissection of the dynamic regulation of biological molecules in highly complex intracellular environments.
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Affiliation(s)
- Byung Hun Lee
- Department of Physics and Astronomy, Seoul National University, Seoul, 08826, Korea
| | - Hye Yoon Park
- Department of Physics and Astronomy, Seoul National University, Seoul, 08826, Korea. .,Institute of Applied Physics, Seoul National University, Seoul, 08826, Korea.
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1714
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Hansen AS, Woringer M, Grimm JB, Lavis LD, Tjian R, Darzacq X. Robust model-based analysis of single-particle tracking experiments with Spot-On. eLife 2018; 7:33125. [PMID: 29300163 PMCID: PMC5809147 DOI: 10.7554/elife.33125] [Citation(s) in RCA: 154] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 01/03/2018] [Indexed: 12/22/2022] Open
Abstract
Single-particle tracking (SPT) has become an important method to bridge biochemistry and cell biology since it allows direct observation of protein binding and diffusion dynamics in live cells. However, accurately inferring information from SPT studies is challenging due to biases in both data analysis and experimental design. To address analysis bias, we introduce 'Spot-On', an intuitive web-interface. Spot-On implements a kinetic modeling framework that accounts for known biases, including molecules moving out-of-focus, and robustly infers diffusion constants and subpopulations from pooled single-molecule trajectories. To minimize inherent experimental biases, we implement and validate stroboscopic photo-activation SPT (spaSPT), which minimizes motion-blur bias and tracking errors. We validate Spot-On using experimentally realistic simulations and show that Spot-On outperforms other methods. We then apply Spot-On to spaSPT data from live mammalian cells spanning a wide range of nuclear dynamics and demonstrate that Spot-On consistently and robustly infers subpopulation fractions and diffusion constants.
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Affiliation(s)
- Anders S Hansen
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of Excellence, University of California, Berkeley, Berkeley, United States.,Howard Hughes Medical Institute, Berkeley, United States
| | - Maxime Woringer
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of Excellence, University of California, Berkeley, Berkeley, United States.,Unité Imagerie et Modélisation, Institut Pasteur, Paris, France.,UPMC Univ Paris 06, Sorbonne Universités, Paris, France
| | - Jonathan B Grimm
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Luke D Lavis
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Robert Tjian
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of Excellence, University of California, Berkeley, Berkeley, United States.,Howard Hughes Medical Institute, Berkeley, United States
| | - Xavier Darzacq
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of Excellence, University of California, Berkeley, Berkeley, United States
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1715
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Hemodynamic Studies for Analyzing the Teratogenic Effects of Drugs in the Zebrafish Embryo. Methods Mol Biol 2018; 1797:487-495. [PMID: 29896711 DOI: 10.1007/978-1-4939-7883-0_27] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Investigations of teratogenic effects of drugs generally involve testing the drug on animals and zebrafish embryo is a commonly used animal model for that purpose. In these studies, cardiovascular function of the animals needs to be evaluated to reveal the influence of exposure on the development of the cardiovascular system as well as on the growth of the whole animal. Here, relevant microscopy imaging and analysis protocols are described to calculate a variety of hemodynamic parameters for zebrafish embryos exposed to clinical drugs.
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1716
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Miño GL, Baabour M, Chertcoff R, Gutkind G, Clément E, Auradou H, Ippolito I. <i>E coli</i> Accumulation behind an Obstacle. ACTA ACUST UNITED AC 2018. [DOI: 10.4236/aim.2018.86030] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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1717
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Abstract
Quantitative fluorescence microscopy techniques are frequently applied to answer fundamental biological questions. Single-molecule RNA imaging methods have enabled the direct observation of the initial steps of the mRNA life cycle in living cells, however, the dynamic mechanisms that regulate mRNA translation are still poorly understood. We have developed an RNA biosensor that can assess the translational state of individual mRNA transcripts with spatiotemporal resolution in living cells. In this chapter, we describe how to perform a TRICK (translating RNA imaging by coat protein knock-off) experiment and specifically focus on a detailed description of our image processing and data analysis procedure.
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Affiliation(s)
- Franka Voigt
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Jan Eglinger
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Jeffrey A Chao
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
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1718
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Du Clos KT, Jiang H. Overcoming hydrodynamic challenges in suspension feeding by juvenile Mya arenaria clams. J R Soc Interface 2018; 15:20170755. [PMID: 29367238 PMCID: PMC5805974 DOI: 10.1098/rsif.2017.0755] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 12/22/2017] [Indexed: 01/16/2023] Open
Abstract
We present some of the few suspension-feeding measurements and to our knowledge the first velocity-field measurements for early post-settlement juvenile bivalve clams. We verify and extend our experimental results with numerical simulations. For 1.8-2.8 mm shell length Mya arenaria clams, pumping rates ranged 0.03-0.22 μl s-1, inhalant siphon Reynolds numbers (Re) ranged 0.16-0.79 and mean inhalant velocities ranged 0.8-3.2 mm s-1 Owing to the low Re at which they pump and the small diameters of their siphons, juvenile clams are subject to unique hydrodynamic challenges, including high siphon resistance and susceptibility to refiltration. At least three features of juvenile clam siphons differentiate them from those of adults-shorter inhalant siphon length, a more rapid increase in inhalant siphon diameter with shell length, and the presence of a prominent exhalant siphon extension. These features are probably adaptations to the challenges of suspension feeding at low Re.
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Affiliation(s)
- Kevin T Du Clos
- Darling Marine Center, School of Marine Sciences, University of Maine, 193 Clarks Cove Road, Walpole, ME 04573-3307, USA
| | - Houshuo Jiang
- Applied Ocean Physics and Engineering Department, Woods Hole Oceanographic Institution, 266 Woods Hole Road, Woods Hole, MA 02543-1535, USA
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1719
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Struntz P, Weiss M. The hitchhiker's guide to quantitative diffusion measurements. Phys Chem Chem Phys 2018; 20:28910-28919. [DOI: 10.1039/c8cp06158k] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Quantitative comparison of three widely used techniques for diffusion measurements, implemented on a light sheet microscope.
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Affiliation(s)
- Philipp Struntz
- Experimental Physics I
- University of Bayreuth
- D-95447 Bayreuth
- Germany
| | - Matthias Weiss
- Experimental Physics I
- University of Bayreuth
- D-95447 Bayreuth
- Germany
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1720
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Gaudel N, Kiesgen de Richter S, Louvet N, Jenny M, Skali-Lami S. Bulk and local rheology in a dense and vibrated granular suspension. Phys Rev E 2017; 96:062905. [PMID: 29347409 DOI: 10.1103/physreve.96.062905] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Indexed: 11/07/2022]
Abstract
In this paper, we investigate experimentally the dynamics of particles in dense granular suspensions when both shear and external vibrations are applied. We study in detail how vibrations affect particle reorganization at the local scale and modify the apparent rheology. The nonlocal nature of the rheology when no vibrations are applied is evidenced, in agreement with previous numerical studies from the literature. It is also shown that vibrations induce structural reorganizations, which tend to homogenize the system and cancel the nonlocal properties.
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Affiliation(s)
- Naïma Gaudel
- Laboratoire d'Énergétique et de Mécanique Théorique et Appliquée (LEMTA), Université de Lorraine-CNRS, UMR 7563, Vandœuvre-lès-Nancy 54505, France
| | - Sébastien Kiesgen de Richter
- Laboratoire d'Énergétique et de Mécanique Théorique et Appliquée (LEMTA), Université de Lorraine-CNRS, UMR 7563, Vandœuvre-lès-Nancy 54505, France
| | - Nicolas Louvet
- Laboratoire d'Énergétique et de Mécanique Théorique et Appliquée (LEMTA), Université de Lorraine-CNRS, UMR 7563, Vandœuvre-lès-Nancy 54505, France
| | - Mathieu Jenny
- Laboratoire d'Énergétique et de Mécanique Théorique et Appliquée (LEMTA), Université de Lorraine-CNRS, UMR 7563, Vandœuvre-lès-Nancy 54505, France
| | - Salaheddine Skali-Lami
- Laboratoire d'Énergétique et de Mécanique Théorique et Appliquée (LEMTA), Université de Lorraine-CNRS, UMR 7563, Vandœuvre-lès-Nancy 54505, France
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1721
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Balabanian L, Berger CL, Hendricks AG. Acetylated Microtubules Are Preferentially Bundled Leading to Enhanced Kinesin-1 Motility. Biophys J 2017; 113:1551-1560. [PMID: 28978447 DOI: 10.1016/j.bpj.2017.08.009] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 08/04/2017] [Accepted: 08/07/2017] [Indexed: 12/29/2022] Open
Abstract
The motor proteins kinesin and dynein transport organelles, mRNA, proteins, and signaling molecules along the microtubule cytoskeleton. In addition to serving as tracks for transport, the microtubule cytoskeleton directs intracellular trafficking by regulating the activity of motor proteins through the organization of the filament network, microtubule-associated proteins, and tubulin posttranslational modifications. However, it is not well understood how these factors influence motor motility, and in vitro assays and live cell observations often produce disparate results. To systematically examine the factors that contribute to cytoskeleton-based regulation of motor protein motility, we extracted intact microtubule networks from cells and tracked the motility of single fluorescently labeled motor proteins on these cytoskeletons. We find that tubulin acetylation alone does not directly affect kinesin-1 motility. However, acetylated microtubules are predominantly bundled, and bundling enhances kinesin run lengths and provides a greater number of available kinesin binding sites. The neuronal MAP tau is also not sensitive to tubulin acetylation, but enriches preferentially on highly curved regions of microtubules where it strongly inhibits kinesin motility. Taken together, these results suggest that the organization of the microtubule network is a key contributor to the regulation of motor-based transport.
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Affiliation(s)
- Linda Balabanian
- Department of Bioengineering, McGill University, Montreal, Québec, Canada
| | - Christopher L Berger
- Department of Molecular Physiology and Biophysics, University of Vermont, Burlington, Vermont
| | - Adam G Hendricks
- Department of Bioengineering, McGill University, Montreal, Québec, Canada.
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1722
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Rodrigo JA, Soto JM, Alieva T. Fast label-free microscopy technique for 3D dynamic quantitative imaging of living cells. BIOMEDICAL OPTICS EXPRESS 2017; 8:5507-5517. [PMID: 29296484 PMCID: PMC5745099 DOI: 10.1364/boe.8.005507] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 10/23/2017] [Accepted: 10/25/2017] [Indexed: 05/03/2023]
Abstract
The refractive index (RI) is an important optical characteristic that is often exploited in label-free microscopy for analysis of biological objects. A technique for 3D RI reconstruction of living cells has to be fast enough to capture the cell dynamics and preferably needs to be compatible with standard wide-field microscopes. To solve this challenging problem, we present a technique that provides fast measurement and processing of data required for real-time 3D visualization of the object RI. Specifically, the 3D RI is reconstructed from the measurement of bright-field intensity images, axially scanned by a high-speed focus tunable lens mounted in front of a sCMOS camera, by using a direct deconvolution approach designed for partially coherent light microscopy in the non-paraxial regime. Both the measurement system and the partially coherent illumination, that provides optical sectioning and speckle-noise suppression, enable compatibility with wide-field microscopes resulting in a competitive and affordable alternative to the current holographic laser microscopes. Our experimental demonstrations show video-rate 3D RI visualization of living bacteria both freely swimming and optically manipulated by using freestyle laser traps allowing for their trapping and transport along 3D trajectories. These results prove that is possible to conduct simultaneous 4D label-free quantitative imaging and optical manipulation of living cells, which is promising for the study of the cell biophysics and biology.
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1723
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Joensuu M, Martínez-Mármol R, Padmanabhan P, Glass NR, Durisic N, Pelekanos M, Mollazade M, Balistreri G, Amor R, Cooper-White JJ, Goodhill GJ, Meunier FA. Visualizing endocytic recycling and trafficking in live neurons by subdiffractional tracking of internalized molecules. Nat Protoc 2017; 12:2590-2622. [PMID: 29189775 DOI: 10.1038/nprot.2017.116] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Our understanding of endocytic pathway dynamics is restricted by the diffraction limit of light microscopy. Although super-resolution techniques can overcome this issue, highly crowded cellular environments, such as nerve terminals, can also dramatically limit the tracking of multiple endocytic vesicles such as synaptic vesicles (SVs), which in turn restricts the analytical dissection of their discrete diffusional and transport states. We recently introduced a pulse-chase technique for subdiffractional tracking of internalized molecules (sdTIM) that allows the visualization of fluorescently tagged molecules trapped in individual signaling endosomes and SVs in presynapses or axons with 30- to 50-nm localization precision. We originally developed this approach for tracking single molecules of botulinum neurotoxin type A, which undergoes activity-dependent internalization and retrograde transport in autophagosomes. This method was then adapted to localize the signaling endosomes containing cholera toxin subunit-B that undergo retrograde transport in axons and to track SVs in the crowded environment of hippocampal presynapses. We describe (i) the construction of a custom-made microfluidic device that enables control over neuronal orientation; (ii) the 3D printing of a perfusion system for sdTIM experiments performed on glass-bottom dishes; (iii) the dissection, culturing and transfection of hippocampal neurons in microfluidic devices; and (iv) guidance on how to perform the pulse-chase experiments and data analysis. In addition, we describe the use of single-molecule-tracking analytical tools to reveal the average and the heterogeneous single-molecule mobility behaviors. We also discuss alternative reagents and equipment that can, in principle, be used for sdTIM experiments and describe how to adapt sdTIM to image nanocluster formation and/or tubulation in early endosomes during sorting events. The procedures described in this protocol take ∼1 week.
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Affiliation(s)
- Merja Joensuu
- Clem Jones Centre for Ageing Dementia Research, The University of Queensland, Brisbane, Queensland, Australia.,Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia.,Minerva Foundation Institute for Medical Research, Helsinki, Finland
| | - Ramon Martínez-Mármol
- Clem Jones Centre for Ageing Dementia Research, The University of Queensland, Brisbane, Queensland, Australia.,Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Pranesh Padmanabhan
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Nick R Glass
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland, Australia
| | - Nela Durisic
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Matthew Pelekanos
- Clem Jones Centre for Ageing Dementia Research, The University of Queensland, Brisbane, Queensland, Australia.,Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Mahdie Mollazade
- Clem Jones Centre for Ageing Dementia Research, The University of Queensland, Brisbane, Queensland, Australia.,Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Giuseppe Balistreri
- Division of General Microbiology, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Rumelo Amor
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Justin J Cooper-White
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland, Australia.,Division of General Microbiology, Department of Biosciences, University of Helsinki, Helsinki, Finland.,School of Chemical Engineering, The University of Queensland, Brisbane, Queensland, Australia.,Materials Science and Engineering Division, CSIRO, Clayton, Victoria, Australia.,UQ Centre for Stem Cell Ageing and Regenerative Engineering, The University of Queensland, Brisbane, Queensland, Australia
| | - Geoffrey J Goodhill
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia.,School of Mathematics and Physics, The University of Queensland, Brisbane, Queensland, Australia
| | - Frédéric A Meunier
- Clem Jones Centre for Ageing Dementia Research, The University of Queensland, Brisbane, Queensland, Australia.,Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
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1724
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Jafferali MH, Figueroa RA, Hasan M, Hallberg E. Spindle associated membrane protein 1 (Samp1) is required for the differentiation of muscle cells. Sci Rep 2017; 7:16655. [PMID: 29192166 PMCID: PMC5709512 DOI: 10.1038/s41598-017-16746-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 10/20/2017] [Indexed: 01/15/2023] Open
Abstract
Muscles are developed and regenerated in a differentiation process called myogenesis, which involves components of the nuclear envelope. We have investigated Samp1 (Spindle Associated Membrane Protein 1), a transmembrane nuclear envelope protein, which interacts with emerin and lamin A, both of which are linked to Emery-Dreifuss muscular dystrophy (EDMD). We found that the levels of Samp1 increased seven-fold during differentiation of mouse C2C12 muscle progenitor cells. To test if Samp1 could have a role in myogenesis we developed stable C2C12 knockdown cell lines expressing short hairpin RNA targeting Samp1 expression. The Samp1 depleted C2C12 cells displayed normal mobility and normal distribution of emerin and lamin A. However, Samp1 depletion increased ERK signaling and completely blocked differentiation of C2C12 cells, which failed to express myogenic marker proteins and failed to form myotubes. The block in myogenesis in Samp1 depleted cells was completely rescued by ectopic expression of RNAi resistant human Samp1, showing that Samp1 is required for muscle differentiation.
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Affiliation(s)
- Mohammed Hakim Jafferali
- Department of Neurochemistry, Stockholm University, Svante Arrhenius väg 16B, SE-106 91, Stockholm, Sweden
| | - Ricardo A Figueroa
- Department of Neurochemistry, Stockholm University, Svante Arrhenius väg 16B, SE-106 91, Stockholm, Sweden
| | - Mehedi Hasan
- Department of Neurochemistry, Stockholm University, Svante Arrhenius väg 16B, SE-106 91, Stockholm, Sweden
| | - Einar Hallberg
- Department of Neurochemistry, Stockholm University, Svante Arrhenius väg 16B, SE-106 91, Stockholm, Sweden.
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1725
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Rueden CT, Schindelin J, Hiner MC, DeZonia BE, Walter AE, Arena ET, Eliceiri KW. ImageJ2: ImageJ for the next generation of scientific image data. BMC Bioinformatics 2017; 18:529. [PMID: 29187165 PMCID: PMC5708080 DOI: 10.1186/s12859-017-1934-z] [Citation(s) in RCA: 3066] [Impact Index Per Article: 438.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 11/14/2017] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND ImageJ is an image analysis program extensively used in the biological sciences and beyond. Due to its ease of use, recordable macro language, and extensible plug-in architecture, ImageJ enjoys contributions from non-programmers, amateur programmers, and professional developers alike. Enabling such a diversity of contributors has resulted in a large community that spans the biological and physical sciences. However, a rapidly growing user base, diverging plugin suites, and technical limitations have revealed a clear need for a concerted software engineering effort to support emerging imaging paradigms, to ensure the software's ability to handle the requirements of modern science. RESULTS We rewrote the entire ImageJ codebase, engineering a redesigned plugin mechanism intended to facilitate extensibility at every level, with the goal of creating a more powerful tool that continues to serve the existing community while addressing a wider range of scientific requirements. This next-generation ImageJ, called "ImageJ2" in places where the distinction matters, provides a host of new functionality. It separates concerns, fully decoupling the data model from the user interface. It emphasizes integration with external applications to maximize interoperability. Its robust new plugin framework allows everything from image formats, to scripting languages, to visualization to be extended by the community. The redesigned data model supports arbitrarily large, N-dimensional datasets, which are increasingly common in modern image acquisition. Despite the scope of these changes, backwards compatibility is maintained such that this new functionality can be seamlessly integrated with the classic ImageJ interface, allowing users and developers to migrate to these new methods at their own pace. CONCLUSIONS Scientific imaging benefits from open-source programs that advance new method development and deployment to a diverse audience. ImageJ has continuously evolved with this idea in mind; however, new and emerging scientific requirements have posed corresponding challenges for ImageJ's development. The described improvements provide a framework engineered for flexibility, intended to support these requirements as well as accommodate future needs. Future efforts will focus on implementing new algorithms in this framework and expanding collaborations with other popular scientific software suites.
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Affiliation(s)
- Curtis T Rueden
- Laboratory for Optical and Computational Instrumentation, University of Wisconsin at Madison, Madison, Wisconsin, USA
| | - Johannes Schindelin
- Laboratory for Optical and Computational Instrumentation, University of Wisconsin at Madison, Madison, Wisconsin, USA
- Morgridge Institute for Research, Madison, Wisconsin, USA
| | - Mark C Hiner
- Laboratory for Optical and Computational Instrumentation, University of Wisconsin at Madison, Madison, Wisconsin, USA
| | - Barry E DeZonia
- Laboratory for Optical and Computational Instrumentation, University of Wisconsin at Madison, Madison, Wisconsin, USA
| | - Alison E Walter
- Laboratory for Optical and Computational Instrumentation, University of Wisconsin at Madison, Madison, Wisconsin, USA
- Morgridge Institute for Research, Madison, Wisconsin, USA
| | - Ellen T Arena
- Laboratory for Optical and Computational Instrumentation, University of Wisconsin at Madison, Madison, Wisconsin, USA
- Morgridge Institute for Research, Madison, Wisconsin, USA
| | - Kevin W Eliceiri
- Laboratory for Optical and Computational Instrumentation, University of Wisconsin at Madison, Madison, Wisconsin, USA.
- Morgridge Institute for Research, Madison, Wisconsin, USA.
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1726
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Rueden CT, Schindelin J, Hiner MC, DeZonia BE, Walter AE, Arena ET, Eliceiri KW. ImageJ2: ImageJ for the next generation of scientific image data. BMC Bioinformatics 2017. [PMID: 29187165 DOI: 10.1186/s12859-017-1934-z.] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND ImageJ is an image analysis program extensively used in the biological sciences and beyond. Due to its ease of use, recordable macro language, and extensible plug-in architecture, ImageJ enjoys contributions from non-programmers, amateur programmers, and professional developers alike. Enabling such a diversity of contributors has resulted in a large community that spans the biological and physical sciences. However, a rapidly growing user base, diverging plugin suites, and technical limitations have revealed a clear need for a concerted software engineering effort to support emerging imaging paradigms, to ensure the software's ability to handle the requirements of modern science. RESULTS We rewrote the entire ImageJ codebase, engineering a redesigned plugin mechanism intended to facilitate extensibility at every level, with the goal of creating a more powerful tool that continues to serve the existing community while addressing a wider range of scientific requirements. This next-generation ImageJ, called "ImageJ2" in places where the distinction matters, provides a host of new functionality. It separates concerns, fully decoupling the data model from the user interface. It emphasizes integration with external applications to maximize interoperability. Its robust new plugin framework allows everything from image formats, to scripting languages, to visualization to be extended by the community. The redesigned data model supports arbitrarily large, N-dimensional datasets, which are increasingly common in modern image acquisition. Despite the scope of these changes, backwards compatibility is maintained such that this new functionality can be seamlessly integrated with the classic ImageJ interface, allowing users and developers to migrate to these new methods at their own pace. CONCLUSIONS Scientific imaging benefits from open-source programs that advance new method development and deployment to a diverse audience. ImageJ has continuously evolved with this idea in mind; however, new and emerging scientific requirements have posed corresponding challenges for ImageJ's development. The described improvements provide a framework engineered for flexibility, intended to support these requirements as well as accommodate future needs. Future efforts will focus on implementing new algorithms in this framework and expanding collaborations with other popular scientific software suites.
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Affiliation(s)
- Curtis T Rueden
- Laboratory for Optical and Computational Instrumentation, University of Wisconsin at Madison, Madison, Wisconsin, USA
| | - Johannes Schindelin
- Laboratory for Optical and Computational Instrumentation, University of Wisconsin at Madison, Madison, Wisconsin, USA.,Morgridge Institute for Research, Madison, Wisconsin, USA
| | - Mark C Hiner
- Laboratory for Optical and Computational Instrumentation, University of Wisconsin at Madison, Madison, Wisconsin, USA
| | - Barry E DeZonia
- Laboratory for Optical and Computational Instrumentation, University of Wisconsin at Madison, Madison, Wisconsin, USA
| | - Alison E Walter
- Laboratory for Optical and Computational Instrumentation, University of Wisconsin at Madison, Madison, Wisconsin, USA.,Morgridge Institute for Research, Madison, Wisconsin, USA
| | - Ellen T Arena
- Laboratory for Optical and Computational Instrumentation, University of Wisconsin at Madison, Madison, Wisconsin, USA.,Morgridge Institute for Research, Madison, Wisconsin, USA
| | - Kevin W Eliceiri
- Laboratory for Optical and Computational Instrumentation, University of Wisconsin at Madison, Madison, Wisconsin, USA. .,Morgridge Institute for Research, Madison, Wisconsin, USA.
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1727
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Mishra S, Vazquez M. A Gal-MµS Device to Evaluate Cell Migratory Response to Combined Galvano-Chemotactic Fields. BIOSENSORS-BASEL 2017; 7:bios7040054. [PMID: 29160793 PMCID: PMC5746777 DOI: 10.3390/bios7040054] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Revised: 11/15/2017] [Accepted: 11/16/2017] [Indexed: 01/10/2023]
Abstract
Electric fields have been studied extensively in biomedical engineering (BME) for numerous regenerative therapies. Recent studies have begun to examine the biological effects of electric fields in combination with other environmental cues, such as tissue-engineered extracellular matrices (ECM), chemical gradient profiles, and time-dependent temperature gradients. In the nervous system, cell migration driven by electrical fields, or galvanotaxis, has been most recently studied in transcranial direct stimulation (TCDS), spinal cord repair and tumor treating fields (TTF). The cell migratory response to galvano-combinatory fields, such as magnetic fields, chemical gradients, or heat shock, has only recently been explored. In the visual system, restoration of vision via cellular replacement therapies has been limited by low numbers of motile cells post-transplantation. Here, the combinatory application of electrical fields with other stimuli to direct cells within transplantable biomaterials and/or host tissues has been understudied. In this work, we developed the Gal-MµS device, a novel microfluidics device capable of examining cell migratory behavior in response to single and combinatory stimuli of electrical and chemical fields. The formation of steady-state, chemical concentration gradients and electrical fields within the Gal-MµS were modeled computationally and verified experimentally within devices fabricated via soft lithography. Further, we utilized real-time imaging within the device to capture cell trajectories in response to electric fields and chemical gradients, individually, as well as in combinatory fields of both. Our data demonstrated that neural cells migrated longer distances and with higher velocities in response to combined galvanic and chemical stimuli than to either field individually, implicating cooperative behavior. These results reveal a biological response to galvano-chemotactic fields that is only partially understood, as well as point towards novel migration-targeted treatments to improve cell-based regenerative therapies.
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Affiliation(s)
- Shawn Mishra
- Department of Biomedical Engineering, City College of New York, New York, NY 10031, USA.
| | - Maribel Vazquez
- Department of Biomedical Engineering, City College of New York, New York, NY 10031, USA.
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1728
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Malerba ME, White CR, Marshall DJ. Eco-energetic consequences of evolutionary shifts in body size. Ecol Lett 2017; 21:54-62. [PMID: 29143436 DOI: 10.1111/ele.12870] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 09/14/2017] [Accepted: 09/30/2017] [Indexed: 11/30/2022]
Abstract
Size imposes physiological and ecological constraints upon all organisms. Theory abounds on how energy flux covaries with body size, yet causal links are often elusive. As a more direct way to assess the role of size, we used artificial selection to evolve the phytoplankton species Dunaliella tertiolecta towards smaller and larger body sizes. Within 100 generations (c. 1 year), we generated a fourfold difference in cell volume among selected lineages. Large-selected populations produced four times the energy than small-selected populations of equivalent total biovolume, but at the cost of much higher volume-specific respiration. These differences in energy utilisation between large (more productive) and small (more energy-efficient) individuals were used to successfully predict ecological performance (r and K) across novel resource regimes. We show that body size determines the performance of a species by mediating its net energy flux, with worrying implications for current trends in size reduction and for global carbon cycles.
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Affiliation(s)
- Martino E Malerba
- Centre of Geometric Biology, School of Biological Sciences, Monash University, Melbourne, Vic., 3800, Australia
| | - Craig R White
- Centre of Geometric Biology, School of Biological Sciences, Monash University, Melbourne, Vic., 3800, Australia
| | - Dustin J Marshall
- Centre of Geometric Biology, School of Biological Sciences, Monash University, Melbourne, Vic., 3800, Australia
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1729
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Ca 2+ signals initiate at immobile IP 3 receptors adjacent to ER-plasma membrane junctions. Nat Commun 2017; 8:1505. [PMID: 29138405 PMCID: PMC5686115 DOI: 10.1038/s41467-017-01644-8] [Citation(s) in RCA: 109] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 10/06/2017] [Indexed: 11/08/2022] Open
Abstract
IP3 receptors (IP3Rs) release Ca2+ from the ER when they bind IP3 and Ca2+. The spatial organization of IP3Rs determines both the propagation of Ca2+ signals between IP3Rs and the selective regulation of cellular responses. Here we use gene editing to fluorescently tag endogenous IP3Rs, and super-resolution microscopy to determine the geography of IP3Rs and Ca2+ signals within living cells. We show that native IP3Rs cluster within ER membranes. Most IP3R clusters are mobile, moved by diffusion and microtubule motors. Ca2+ signals are generated by a small population of immobile IP3Rs. These IP3Rs are licensed to respond, but they do not readily mix with mobile IP3Rs. The licensed IP3Rs reside alongside ER-plasma membrane junctions where STIM1, which regulates store-operated Ca2+ entry, accumulates after depletion of Ca2+ stores. IP3Rs tethered close to ER-plasma membrane junctions are licensed to respond and optimally placed to be activated by endogenous IP3 and to regulate Ca2+ entry. IP3 receptors mediate Ca2+ release from the endoplasmic reticulum. Here the authors show that only a small fraction of IP3 receptors initiate Ca2+ signals; these immobile IP3 receptors adjacent to the plasma membrane are optimally placed to control STIM1-dependent Ca2+ entry.
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1730
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Hsieh TS, Chen YJ, Chang CL, Lee WR, Liou J. Cortical actin contributes to spatial organization of ER-PM junctions. Mol Biol Cell 2017; 28:3171-3180. [PMID: 28954864 PMCID: PMC5687020 DOI: 10.1091/mbc.e17-06-0377] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 09/18/2017] [Accepted: 09/20/2017] [Indexed: 01/16/2023] Open
Abstract
Endoplasmic reticulum-plasma membrane (ER-PM) junctions mediate crucial activities ranging from Ca2+ signaling to lipid metabolism. Spatial organization of ER-PM junctions may modulate the extent and location of these cellular activities. However, the morphology and distribution of ER-PM junctions are not well characterized. Using photoactivated localization microscopy, we reveal that the contact area of single ER-PM junctions is mainly oblong with the dimensions of ∼120 nm × ∼80 nm in HeLa cells. Using total internal reflection fluorescence microscopy and structure illumination microscopy, we show that cortical actin contributes to spatial distribution and stability of ER-PM junctions. Further functional assays suggest that intact F-actin architecture is required for phosphatidylinositol 4,5-bisphosphate homeostasis mediated by Nir2 at ER-PM junctions. Together, our study provides quantitative information on spatial organization of ER-PM junctions that is in part regulated by F-actin. We envision that functions of ER-PM junctions can be differentially regulated through dynamic actin remodeling during cellular processes.
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Affiliation(s)
- Ting-Sung Hsieh
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Yu-Ju Chen
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Chi-Lun Chang
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Wan-Ru Lee
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Jen Liou
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390
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1731
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Liu P, Weinreb V, Ridilla M, Betts L, Patel P, de Silva AM, Thompson NL, Jacobson K. Rapid, directed transport of DC-SIGN clusters in the plasma membrane. SCIENCE ADVANCES 2017; 3:eaao1616. [PMID: 29134199 PMCID: PMC5677337 DOI: 10.1126/sciadv.aao1616] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 10/16/2017] [Indexed: 05/12/2023]
Abstract
C-type lectins, including dendritic cell-specific intercellular adhesion molecule-3-grabbing nonintegrin (DC-SIGN), are all-purpose pathogen receptors that exist in nanoclusters in plasma membranes of dendritic cells. A small fraction of these clusters, obvious from the videos, can undergo rapid, directed transport in the plane of the plasma membrane at average speeds of more than 1 μm/s in both dendritic cells and MX DC-SIGN murine fibroblasts ectopically expressing DC-SIGN. Surprisingly, instantaneous speeds can be considerably greater. In MX DC-SIGN cells, many cluster trajectories are colinear with microtubules that reside close to the ventral membrane, and the microtubule-depolymerizing drug, nocodazole, markedly reduced the areal density of directed movement trajectories, suggesting a microtubule motor-driven transport mechanism; by contrast, latrunculin A, which affects the actin network, did not depress this movement. Rapid, retrograde movement of DC-SIGN may be an efficient mechanism for bringing bound pathogen on the leading edge and projections of dendritic cells to the perinuclear region for internalization and processing. Dengue virus bound to DC-SIGN on dendritic projections was rapidly transported toward the cell center. The existence of this movement within the plasma membrane points to an unexpected lateral transport mechanism in mammalian cells and challenges our current concepts of cortex-membrane interactions.
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Affiliation(s)
- Ping Liu
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Violetta Weinreb
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Marc Ridilla
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Laurie Betts
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Pratik Patel
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Aravinda M. de Silva
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Nancy L. Thompson
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ken Jacobson
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Corresponding author.
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1732
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Horvathova I, Voigt F, Kotrys AV, Zhan Y, Artus-Revel CG, Eglinger J, Stadler MB, Giorgetti L, Chao JA. The Dynamics of mRNA Turnover Revealed by Single-Molecule Imaging in Single Cells. Mol Cell 2017; 68:615-625.e9. [PMID: 29056324 DOI: 10.1016/j.molcel.2017.09.030] [Citation(s) in RCA: 123] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 09/08/2017] [Accepted: 09/21/2017] [Indexed: 01/06/2023]
Abstract
RNA degradation plays a fundamental role in regulating gene expression. In order to characterize the spatiotemporal dynamics of RNA turnover in single cells, we developed a fluorescent biosensor based on dual-color, single-molecule RNA imaging that allows intact transcripts to be distinguished from stabilized degradation intermediates. Using this method, we measured mRNA decay in single cells and found that individual degradation events occur independently within the cytosol and are not enriched within processing bodies. We show that slicing of an mRNA targeted for endonucleolytic cleavage by the RNA-induced silencing complex can be observed in real time in living cells. This methodology provides a framework for investigating the entire life history of individual mRNAs from birth to death in single cells.
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Affiliation(s)
- Ivana Horvathova
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland; University of Basel, 4003 Basel, Switzerland
| | - Franka Voigt
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Anna V Kotrys
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Yinxiu Zhan
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland; University of Basel, 4003 Basel, Switzerland
| | | | - Jan Eglinger
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Michael B Stadler
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland; Swiss Institute of Bioinformatics, 4058 Basel, Switzerland
| | - Luca Giorgetti
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Jeffrey A Chao
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland.
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1733
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Effects of predator lipids on dinoflagellate defence mechanisms - increased bioluminescence capacity. Sci Rep 2017; 7:13104. [PMID: 29026130 PMCID: PMC5638803 DOI: 10.1038/s41598-017-13293-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 09/20/2017] [Indexed: 11/08/2022] Open
Abstract
Short flashes of blue light (bioluminescence) from dinoflagellates can reduce copepod grazing of light-emitting cells. Other protective strategies against grazing are toxicity, reduced cell chain length and altered swimming patterns in different phytoplankton. Both toxicity and bioluminescence capacity in dinoflagellates decrease in copepod-free cultures, but toxin production can be restored in response to chemical alarm signals from copepods, copepodamides. Here we show that strains of the dinoflagellates Lingulodinium polyedra and Alexandrium tamarense, kept in culture for 14 and 9 years respectively, are capable of increasing their total bioluminescence capacity in response to copepodamides. The luminescence response to mechanical stimulation with air bubbles also increases significantly in L. polyedra after exposure to copepodamides. Effects on size, swimming speed and rate of change of direction in L. polyedra and A. tamarense were not detected, suggesting that post-encounter mechanisms such as bioluminescence and toxin production may constitute the dominating line of defence in these taxa. To our knowledge, this study provides the first evidence of changes in bioluminescence physiology as a response to chemical cues from natural enemies and emphasizes the importance of bioluminescence as an anti-grazing strategy.
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1734
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Organs on chip approach: a tool to evaluate cancer -immune cells interactions. Sci Rep 2017; 7:12737. [PMID: 28986543 PMCID: PMC5630614 DOI: 10.1038/s41598-017-13070-3] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 07/27/2017] [Indexed: 11/08/2022] Open
Abstract
In this paper we discuss the applicability of numerical descriptors and statistical physics concepts to characterize complex biological systems observed at microscopic level through organ on chip approach. To this end, we employ data collected on a microfluidic platform in which leukocytes can move through suitably built channels toward their target. Leukocyte behavior is recorded by standard time lapse imaging. In particular, we analyze three groups of human peripheral blood mononuclear cells (PBMC): heterozygous mutants (in which only one copy of the FPR1 gene is normal), homozygous mutants (in which both alleles encoding FPR1 are loss-of-function variants) and cells from 'wild type' donors (with normal expression of FPR1). We characterize the migration of these cells providing a quantitative confirmation of the essential role of FPR1 in cancer chemotherapy response. Indeed wild type PBMC perform biased random walks toward chemotherapy-treated cancer cells establishing persistent interactions with them. Conversely, heterozygous mutants present a weaker bias in their motion and homozygous mutants perform rather uncorrelated random walks, both failing to engage with their targets. We next focus on wild type cells and study the interactions of leukocytes with cancerous cells developing a novel heuristic procedure, inspired by Lyapunov stability in dynamical systems.
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1735
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Jacquemet G, Paatero I, Carisey AF, Padzik A, Orange JS, Hamidi H, Ivaska J. FiloQuant reveals increased filopodia density during breast cancer progression. J Cell Biol 2017; 216:3387-3403. [PMID: 28765364 PMCID: PMC5626550 DOI: 10.1083/jcb.201704045] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 06/01/2017] [Accepted: 07/07/2017] [Indexed: 11/22/2022] Open
Abstract
Defective filopodia formation is linked to pathologies such as cancer, wherein actively protruding filopodia, at the invasive front, accompany cancer cell dissemination. Despite wide biological significance, delineating filopodia function in complex systems remains challenging and is particularly hindered by lack of compatible methods to quantify filopodia properties. Here, we present FiloQuant, a freely available ImageJ plugin, to detect filopodia-like protrusions in both fixed- and live-cell microscopy data. We demonstrate that FiloQuant can extract quantifiable information, including protrusion dynamics, density, and length, from multiple cell types and in a range of microenvironments. In cellular models of breast ductal carcinoma in situ, we reveal a link between filopodia formation at the cell-matrix interface, in collectively invading cells and 3D tumor spheroids, and the in vitro invasive capacity of the carcinoma. Finally, using intravital microscopy, we observe that tumor spheroids display filopodia in vivo, supporting a potential role for these protrusions during tumorigenesis.
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Affiliation(s)
- Guillaume Jacquemet
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
| | - Ilkka Paatero
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
| | - Alexandre F Carisey
- Center for Human Immunobiology, Texas Children's Hospital, Houston, TX
- Department of Pediatrics, Pathology and Immunology, Baylor College of Medicine, Houston, TX
| | - Artur Padzik
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
| | - Jordan S Orange
- Center for Human Immunobiology, Texas Children's Hospital, Houston, TX
- Department of Pediatrics, Pathology and Immunology, Baylor College of Medicine, Houston, TX
| | - Hellyeh Hamidi
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
| | - Johanna Ivaska
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
- Department of Biochemistry, University of Turku, Turku, Finland
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1736
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Niederhuber MJ, Lambert TJ, Yapp C, Silver PA, Polka JK. Superresolution microscopy of the β-carboxysome reveals a homogeneous matrix. Mol Biol Cell 2017; 28:2734-2745. [PMID: 28963440 PMCID: PMC5620380 DOI: 10.1091/mbc.e17-01-0069] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 07/26/2017] [Accepted: 08/02/2017] [Indexed: 11/11/2022] Open
Abstract
Carbon fixation in cyanobacteria makes a major contribution to the global carbon cycle. The cyanobacterial carboxysome is a proteinaceous microcompartment that protects and concentrates the carbon-fixing enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) in a paracrystalline lattice, making it possible for these organisms to fix CO2 from the atmosphere. The protein responsible for the organization of this lattice in beta-type carboxysomes of the freshwater cyanobacterium Synechococcus elongatus, CcmM, occurs in two isoforms thought to localize differentially within the carboxysome matrix. Here we use wide-field time-lapse and three-dimensional structured illumination microscopy (3D-SIM) to study the recruitment and localization of these two isoforms. We demonstrate that this superresolution technique is capable of distinguishing the localizations of the outer protein shell of the carboxysome and its internal cargo. We develop an automated analysis pipeline to analyze and quantify 3D-SIM images and generate a population-level description of the carboxysome shell protein, RuBisCO, and CcmM isoform localization. We find that both CcmM isoforms have similar spatial and temporal localization, prompting a revised model of the internal arrangement of the β-carboxysome.
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Affiliation(s)
- Matthew J Niederhuber
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115
| | - Talley J Lambert
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
| | - Clarence Yapp
- Image and Data Analysis Core, Harvard Medical School, Boston, MA 02115
| | - Pamela A Silver
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115
| | - Jessica K Polka
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115
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1737
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Landino J, Norris SR, Li M, Ballister ER, Lampson MA, Ohi R. Two mechanisms coordinate the recruitment of the chromosomal passenger complex to the plane of cell division. Mol Biol Cell 2017; 28:3634-3646. [PMID: 28954866 PMCID: PMC5706991 DOI: 10.1091/mbc.e17-06-0399] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 09/18/2017] [Accepted: 09/22/2017] [Indexed: 11/11/2022] Open
Abstract
Proper positioning of the chromosomal passenger complex (CPC) at the cell division plane is required for cytokinesis. We show here that CPC targeting to the equatorial cortex depends on both the kinesin MKlp2 and a direct interaction with actin. These recruitment mechanisms converge to promote successful cleavage furrow ingression. During cytokinesis, the chromosomal passenger complex (CPC) promotes midzone organization, specifies the cleavage plane, and regulates furrow contractility. The localizations of the CPC are coupled to its cytokinetic functions. At the metaphase-to-anaphase transition, the CPC dissociates from centromeres and localizes to midzone microtubules and the equatorial cortex. CPC relocalization to the cell middle is thought to depend on MKlp2-driven, plus end–directed transport. In support of this idea, MKlp2 depletion impairs cytokinesis; however, cytokinesis failure stems from furrow regression rather than failed initiation of furrowing. This suggests that an alternative mechanism(s) may concentrate the CPC at the division plane. We show here that direct actin binding, via the inner centromere protein (INCENP), enhances CPC enrichment at the equatorial cortex, thus acting in tandem with MKlp2. INCENP overexpression rescues furrowing in MKlp2-depleted cells in an INCENP-actin binding–dependent manner. Using live-cell imaging, we also find that MKlp2-dependent targeting of the CPC is biphasic. MKlp2 targets the CPC to the anti-parallel microtubule overlap of the midzone, after which the MKlp2-CPC complex moves in a nondirected manner. Collectively, our work suggests that both actin binding and MKlp2-dependent midzone targeting cooperate to precisely position the CPC during mitotic exit, and that these pathways converge to ensure successful cleavage furrow ingression.
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Affiliation(s)
- Jennifer Landino
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN 37232
| | - Stephen R Norris
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN 37232
| | - Muyi Li
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104
| | - Edward R Ballister
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104
| | - Michael A Lampson
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104
| | - Ryoma Ohi
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN 37232 .,Department of Cell and Developmental Biology and Life Sciences Institute, University of Michigan Medical School, Ann Arbor, MI 48109
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1738
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Duchi S, Piccinini F, Pierini M, Bevilacqua A, Torre ML, Lucarelli E, Santi S. A new holistic 3D non-invasive analysis of cellular distribution and motility on fibroin-alginate microcarriers using light sheet fluorescent microscopy. PLoS One 2017; 12:e0183336. [PMID: 28817694 PMCID: PMC5560673 DOI: 10.1371/journal.pone.0183336] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 08/02/2017] [Indexed: 12/12/2022] Open
Abstract
Cell interaction with biomaterials is one of the keystones to developing medical devices for tissue engineering applications. Biomaterials are the scaffolds that give three-dimensional support to the cells, and are vectors that deliver the cells to the injured tissue requiring repair. Features of biomaterials can influence the behaviour of the cells and consequently the efficacy of the tissue-engineered product. The adhesion, distribution and motility of the seeded cells onto the scaffold represent key aspects, and must be evaluated in vitro during the product development, especially when the efficacy of a specific tissue-engineered product depends on viable and functional cell loading. In this work, we propose a non-invasive and non-destructive imaging analysis for investigating motility, viability and distribution of Mesenchymal Stem Cells (MSCs) on silk fibroin-based alginate microcarriers, to test the adhesion capacity of the fibroin coating onto alginate which is known to be unsuitable for cell adhesion. However, in depth characterization of the biomaterial is beyond the scope of this paper. Scaffold-loaded MSCs were stained with Calcein-AM and Ethidium homodimer-1 to detect live and dead cells, respectively, and counterstained with Hoechst to label cell nuclei. Time-lapse Light Sheet Fluorescent Microscopy (LSFM) was then used to produce three-dimensional images of the entire cells-loaded fibroin/alginate microcarriers. In order to quantitatively track the cell motility over time, we also developed an open source user friendly software tool called Fluorescent Cell Tracker in Three-Dimensions (F-Tracker3D). Combining LSFM with F-Tracker3D we were able for the first time to assess the distribution and motility of stem cells in a non-invasive, non-destructive, quantitative, and three-dimensional analysis of the entire surface of the cell-loaded scaffold. We therefore propose this imaging technique as an innovative holistic tool for monitoring cell-biomaterial interactions, and as a tool for the design, fabrication and functionalization of a scaffold as a medical device.
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Affiliation(s)
- Serena Duchi
- Osteoarticolar Regeneration Laboratory, Rizzoli Orthopaedic Institute, Bologna, Italy
- Department of Surgery, St Vincent’s Hospital, University of Melbourne, Fitzroy, Victoria, Australia
| | - Filippo Piccinini
- Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) S.r.l., IRCCS, Meldola (FC), Italy
| | - Michela Pierini
- Osteoarticolar Regeneration Laboratory, Rizzoli Orthopaedic Institute, Bologna, Italy
- Department of Biomedical and Neuromotor Sciences (DIBINEM), Alma Mater Studiorum University of Bologna, Bologna, Italy
| | - Alessandro Bevilacqua
- Advanced Research Center on Electronic Systems “Ercole De Castro” (ARCES), Alma Mater Studiorum University of Bologna, Bologna, Italy
- Department of Computer Science and Engineering (DISI), Alma Mater Studiorum University of Bologna, Bologna, Italy
| | - Maria Luisa Torre
- Cell Delivery System Lab, Department of Drug Sciences, University of Pavia, Pavia, Italy
| | - Enrico Lucarelli
- Osteoarticolar Regeneration Laboratory, Rizzoli Orthopaedic Institute, Bologna, Italy
| | - Spartaco Santi
- Institute of Molecular Genetics (CNR), Bologna, Italy
- SC Laboratory of Musculoskeletal Cell Biology, Rizzoli Orthopaedic Institute, Bologna, Italy
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1739
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Snider CE, Willet AH, Chen JS, Arpağ G, Zanic M, Gould KL. Phosphoinositide-mediated ring anchoring resists perpendicular forces to promote medial cytokinesis. J Cell Biol 2017; 216:3041-3050. [PMID: 28784611 PMCID: PMC5626552 DOI: 10.1083/jcb.201705070] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 06/23/2017] [Accepted: 07/07/2017] [Indexed: 11/27/2022] Open
Abstract
Altering phosphoinositide composition through deletion of efr3, a PI4 kinase scaffold, results in type V myosin-dependent cytokinetic ring sliding in Schizosaccharomyces pombe. Membrane-binding proteins contribute to ring anchoring to resist perpendicular forces and thereby promote medial cytokinesis. Many eukaryotic cells divide by assembling and constricting an actin- and myosin-based contractile ring (CR) that is physically linked to the plasma membrane (PM). In this study, we report that Schizosaccharomyces pombe cells lacking efr3, which encodes a conserved PM scaffold for the phosphatidylinositol-4 kinase Stt4, build CRs that can slide away from the cell middle during anaphase in a myosin V–dependent manner. The Efr3-dependent CR-anchoring mechanism is distinct from previously reported pathways dependent on the Fes/CIP4 homology Bin-Amphiphysin-Rvs167 (F-BAR) protein Cdc15 and paxillin Pxl1. In efr3Δ, the concentrations of several membrane-binding proteins were reduced in the CR and/or on the PM. Our results suggest that proper PM lipid composition is important to stabilize the central position of the CR and resist myosin V–based forces to promote the fidelity of cell division.
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Affiliation(s)
- Chloe E Snider
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN
| | - Alaina H Willet
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN
| | - Jun-Song Chen
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN
| | - Göker Arpağ
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN
| | - Marija Zanic
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN
| | - Kathleen L Gould
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN
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1740
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Bauer KE, Kiebler MA, Segura I. Visualizing RNA granule transport and translation in living neurons. Methods 2017. [DOI: 10.1016/j.ymeth.2017.06.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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1741
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Icha J, Weber M, Waters JC, Norden C. Phototoxicity in live fluorescence microscopy, and how to avoid it. Bioessays 2017; 39. [DOI: 10.1002/bies.201700003] [Citation(s) in RCA: 202] [Impact Index Per Article: 28.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Jaroslav Icha
- Max Planck Institute of Molecular Cell Biology and Genetics; Dresden; Germany
| | - Michael Weber
- Department of Cell Biology; Harvard Medical School; Boston MA USA
| | | | - Caren Norden
- Max Planck Institute of Molecular Cell Biology and Genetics; Dresden; Germany
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1742
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Abstract
It has been assumed that DNA synthesis by the leading- and lagging-strand polymerases in the replisome must be coordinated to avoid the formation of significant gaps in the nascent strands. Using real-time single-molecule analysis, we establish that leading- and lagging-strand DNA polymerases function independently within a single replisome. Although average rates of DNA synthesis on leading and lagging strands are similar, individual trajectories of both DNA polymerases display stochastically switchable rates of synthesis interspersed with distinct pauses. DNA unwinding by the replicative helicase may continue during such pauses, but a self-governing mechanism, where helicase speed is reduced by ∼80%, permits recoupling of polymerase to helicase. These features imply a more dynamic, kinetically discontinuous replication process, wherein contacts within the replisome are continually broken and reformed. We conclude that the stochastic behavior of replisome components ensures complete DNA duplication without requiring coordination of leading- and lagging-strand synthesis. PAPERCLIP.
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1743
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Shepherd DJ, Tsai SY, Cappucci SP, Wu JY, Farrer RG, Kartje GL. The Subventricular Zone Response to Stroke Is Not a Therapeutic Target of Anti-Nogo-A Immunotherapy. J Neuropathol Exp Neurol 2017; 76:683-696. [DOI: 10.1093/jnen/nlx050] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Affiliation(s)
- Daniel J. Shepherd
- From the Loyola University Health Sciences Division, Maywood, Illinois (DJS, SPC, GLK); and Edward Hines Jr. Veterans Affairs Hospital, Research Service, Hines, Illinois (DJS, S-YT, SPC, JYW, RGF, GLK)
| | - Shih-Yen Tsai
- From the Loyola University Health Sciences Division, Maywood, Illinois (DJS, SPC, GLK); and Edward Hines Jr. Veterans Affairs Hospital, Research Service, Hines, Illinois (DJS, S-YT, SPC, JYW, RGF, GLK)
| | - Stefanie P. Cappucci
- From the Loyola University Health Sciences Division, Maywood, Illinois (DJS, SPC, GLK); and Edward Hines Jr. Veterans Affairs Hospital, Research Service, Hines, Illinois (DJS, S-YT, SPC, JYW, RGF, GLK)
| | - Joanna Y. Wu
- From the Loyola University Health Sciences Division, Maywood, Illinois (DJS, SPC, GLK); and Edward Hines Jr. Veterans Affairs Hospital, Research Service, Hines, Illinois (DJS, S-YT, SPC, JYW, RGF, GLK)
| | - Robert G. Farrer
- From the Loyola University Health Sciences Division, Maywood, Illinois (DJS, SPC, GLK); and Edward Hines Jr. Veterans Affairs Hospital, Research Service, Hines, Illinois (DJS, S-YT, SPC, JYW, RGF, GLK)
| | - Gwendolyn L. Kartje
- From the Loyola University Health Sciences Division, Maywood, Illinois (DJS, SPC, GLK); and Edward Hines Jr. Veterans Affairs Hospital, Research Service, Hines, Illinois (DJS, S-YT, SPC, JYW, RGF, GLK)
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1744
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Owen LM, Adhikari AS, Patel M, Grimmer P, Leijnse N, Kim MC, Notbohm J, Franck C, Dunn AR. A cytoskeletal clutch mediates cellular force transmission in a soft, three-dimensional extracellular matrix. Mol Biol Cell 2017; 28:1959-1974. [PMID: 28592635 PMCID: PMC5541846 DOI: 10.1091/mbc.e17-02-0102] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 05/26/2017] [Accepted: 05/31/2017] [Indexed: 01/08/2023] Open
Abstract
The ability of cells to impart forces and deformations on their surroundings underlies cell migration and extracellular matrix (ECM) remodeling and is thus an essential aspect of complex, metazoan life. Previous work has resulted in a refined understanding, commonly termed the molecular clutch model, of how cells adhering to flat surfaces such as a microscope coverslip transmit cytoskeletally generated forces to their surroundings. Comparatively less is known about how cells adhere to and exert forces in soft, three-dimensional (3D), and structurally heterogeneous ECM environments such as occur in vivo. We used time-lapse 3D imaging and quantitative image analysis to determine how the actin cytoskeleton is mechanically coupled to the surrounding matrix for primary dermal fibroblasts embedded in a 3D fibrin matrix. Under these circumstances, the cytoskeletal architecture is dominated by contractile actin bundles attached at their ends to large, stable, integrin-based adhesions. Time-lapse imaging reveals that α-actinin-1 puncta within actomyosin bundles move more quickly than the paxillin-rich adhesion plaques, which in turn move more quickly than the local matrix, an observation reminiscent of the molecular clutch model. However, closer examination did not reveal a continuous rearward flow of the actin cytoskeleton over slower moving adhesions. Instead, we found that a subset of stress fibers continuously elongated at their attachment points to integrin adhesions, providing stable, yet structurally dynamic coupling to the ECM. Analytical modeling and numerical simulation provide a plausible physical explanation for this result and support a picture in which cells respond to the effective stiffness of local matrix attachment points. The resulting dynamic equilibrium can explain how cells maintain stable, contractile connections to discrete points within ECM during cell migration, and provides a plausible means by which fibroblasts contract provisional matrices during wound healing.
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Affiliation(s)
- Leanna M Owen
- Biophysics, Stanford University, Stanford, CA 94305
- Chemical Engineering, Stanford University, Stanford, CA 94305
| | | | - Mohak Patel
- School of Engineering, Brown University, Providence, RI 02912
| | - Peter Grimmer
- Department of Engineering Physics, University of Wisconsin-Madison, Madison, WI 53711
| | | | - Min Cheol Kim
- Chemical Engineering, Stanford University, Stanford, CA 94305
| | - Jacob Notbohm
- Department of Engineering Physics, University of Wisconsin-Madison, Madison, WI 53711
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1745
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Samadder P, Suchánková T, Hylse O, Khirsariya P, Nikulenkov F, Drápela S, Straková N, Vaňhara P, Vašíčková K, Kolářová H, Binó L, Bittová M, Ovesná P, Kollár P, Fedr R, Ešner M, Jaroš J, Hampl A, Krejčí L, Paruch K, Souček K. Synthesis and Profiling of a Novel Potent Selective Inhibitor of CHK1 Kinase Possessing Unusual N-trifluoromethylpyrazole Pharmacophore Resistant to Metabolic N-dealkylation. Mol Cancer Ther 2017; 16:1831-1842. [PMID: 28619751 DOI: 10.1158/1535-7163.mct-17-0018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 05/21/2017] [Accepted: 06/08/2017] [Indexed: 11/16/2022]
Abstract
Checkpoint-mediated dependency of tumor cells can be deployed to selectively kill them without substantial toxicity to normal cells. Specifically, loss of CHK1, a serine threonine kinase involved in the surveillance of the G2-M checkpoint in the presence of replication stress inflicted by DNA-damaging drugs, has been reported to dramatically influence the viability of tumor cells. CHK1's pivotal role in maintaining genomic stability offers attractive opportunity for increasing the selectivity, effectivity, and reduced toxicity of chemotherapy. Some recently identified CHK1 inhibitors entered clinical trials in combination with DNA antimetabolites. Herein, we report synthesis and profiling of MU380, a nontrivial analogue of clinically profiled compound SCH900776 possessing the highly unusual N-trifluoromethylpyrazole motif, which was envisioned not to undergo metabolic oxidative dealkylation and thereby provide greater robustness to the compound. MU380 is a selective and potent inhibitor of CHK1 which sensitizes a variety of tumor cell lines to hydroxyurea or gemcitabine up to 10 times. MU380 shows extended inhibitory effects in cells, and unlike SCH900776, does not undergo in vivo N-dealkylation to the significantly less selective metabolite. Compared with SCH900776, MU380 in combination with GEM causes higher accumulation of DNA damage in tumor cells and subsequent enhanced cell death, and is more efficacious in the A2780 xenograft mouse model. Overall, MU380 represents a novel state-of-the-art CHK1 inhibitor with high potency, selectivity, and improved metabolic robustness to oxidative N-dealkylation. Mol Cancer Ther; 16(9); 1831-42. ©2017 AACR.
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Affiliation(s)
- Pounami Samadder
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic.,National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic.,International Clinical Research Center, Center for Biomolecular and Cellular Engineering, St. Anne's University Hospital in Brno, Brno, Czech Republic
| | - Tereza Suchánková
- Department of Cytokinetics, Institute of Biophysics CAS, Brno, Czech Republic
| | - Ondřej Hylse
- Department of Chemistry, CZ Openscreen, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Prashant Khirsariya
- International Clinical Research Center, Center for Biomolecular and Cellular Engineering, St. Anne's University Hospital in Brno, Brno, Czech Republic.,Department of Chemistry, CZ Openscreen, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Fedor Nikulenkov
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic.,International Clinical Research Center, Center for Biomolecular and Cellular Engineering, St. Anne's University Hospital in Brno, Brno, Czech Republic
| | - Stanislav Drápela
- Department of Cytokinetics, Institute of Biophysics CAS, Brno, Czech Republic
| | - Nicol Straková
- International Clinical Research Center, Center for Biomolecular and Cellular Engineering, St. Anne's University Hospital in Brno, Brno, Czech Republic.,Department of Cytokinetics, Institute of Biophysics CAS, Brno, Czech Republic
| | - Petr Vaňhara
- International Clinical Research Center, Center for Biomolecular and Cellular Engineering, St. Anne's University Hospital in Brno, Brno, Czech Republic.,Institute of Biostatistics and Analyses, Masaryk University, Brno, Czech Republic
| | - Kateřina Vašíčková
- International Clinical Research Center, Center for Biomolecular and Cellular Engineering, St. Anne's University Hospital in Brno, Brno, Czech Republic.,Institute of Biostatistics and Analyses, Masaryk University, Brno, Czech Republic
| | - Hana Kolářová
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic.,National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic.,International Clinical Research Center, Center for Biomolecular and Cellular Engineering, St. Anne's University Hospital in Brno, Brno, Czech Republic
| | - Lucia Binó
- International Clinical Research Center, Center for Biomolecular and Cellular Engineering, St. Anne's University Hospital in Brno, Brno, Czech Republic.,Department of Cytokinetics, Institute of Biophysics CAS, Brno, Czech Republic
| | - Miroslava Bittová
- International Clinical Research Center, Center for Biomolecular and Cellular Engineering, St. Anne's University Hospital in Brno, Brno, Czech Republic.,Department of Chemistry, CZ Openscreen, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Petra Ovesná
- Department of Cytokinetics, Institute of Biophysics CAS, Brno, Czech Republic.,Department of Human Pharmacology and Toxicology, Faculty of Pharmacy, University of Veterinary and Pharmaceutical Sciences, Brno, Czech Republic
| | - Peter Kollár
- Cellular Imaging Core Facility - CELLIM, CEITEC Masaryk University, Brno, Czech Republic
| | - Radek Fedr
- International Clinical Research Center, Center for Biomolecular and Cellular Engineering, St. Anne's University Hospital in Brno, Brno, Czech Republic.,Department of Cytokinetics, Institute of Biophysics CAS, Brno, Czech Republic
| | - Milan Ešner
- Institute of Biostatistics and Analyses, Masaryk University, Brno, Czech Republic.,Cellular Imaging Core Facility - CELLIM, CEITEC Masaryk University, Brno, Czech Republic
| | - Josef Jaroš
- International Clinical Research Center, Center for Biomolecular and Cellular Engineering, St. Anne's University Hospital in Brno, Brno, Czech Republic.,Institute of Biostatistics and Analyses, Masaryk University, Brno, Czech Republic
| | - Aleš Hampl
- International Clinical Research Center, Center for Biomolecular and Cellular Engineering, St. Anne's University Hospital in Brno, Brno, Czech Republic.,Institute of Biostatistics and Analyses, Masaryk University, Brno, Czech Republic
| | - Lumír Krejčí
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic. .,National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic.,International Clinical Research Center, Center for Biomolecular and Cellular Engineering, St. Anne's University Hospital in Brno, Brno, Czech Republic
| | - Kamil Paruch
- International Clinical Research Center, Center for Biomolecular and Cellular Engineering, St. Anne's University Hospital in Brno, Brno, Czech Republic. .,Department of Chemistry, CZ Openscreen, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Karel Souček
- International Clinical Research Center, Center for Biomolecular and Cellular Engineering, St. Anne's University Hospital in Brno, Brno, Czech Republic. .,Department of Cytokinetics, Institute of Biophysics CAS, Brno, Czech Republic.,Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
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1746
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Longbottom BW, Somuncuoğlu B, Punter JJ, Longbottom S, Bon SAF. Roughening up polymer microspheres and their diffusion in a liquid. SOFT MATTER 2017; 13:4285-4293. [PMID: 28573302 DOI: 10.1039/c7sm00589j] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
A simple, versatile approach for the roughening of polymer microparticles surfaces via a deformation technique in the presence of an inorganic matrix is presented here. The process consists of straightforward steps: (1) preparation of a bicomposite colloidal sol, that is polymer particles and inorganic particles, dispersed in a liquid, (2) drying of the mixture onto a suitable hard substrate, (3) heating the dried film above the glass transition temperature of the polymer, and (4) re-dispersion and chemical etching of the inorganic medium. The primary driver is capillary imbibition of the polymer melt into the inorganic colloidal template. In addition, 2D particle tracking experiments of dispersed rough particles in water were performed to probe the diffusional behaviour of the roughened objects in comparison with their smooth precursors. We show that, despite large scale roughness (up to 10% asperity size with respect to particle diameter), Stokes law is obeyed and the particle motion can be modelled simply with the Stokes-Einstein-Sutherland relation.
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Affiliation(s)
- Brooke W Longbottom
- The Department of Chemistry, The University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK. www.bonlab.info
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1747
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Babel L, Grunewald M, Lehn R, Langhans M, Meckel T. Direct evidence for cell adhesion-mediated radioresistance (CAM-RR) on the level of individual integrin β1 clusters. Sci Rep 2017; 7:3393. [PMID: 28611417 PMCID: PMC5469790 DOI: 10.1038/s41598-017-03414-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2017] [Accepted: 04/13/2017] [Indexed: 01/30/2023] Open
Abstract
The cellular interaction with the extracellular matrix (ECM) modulates many key processes such as proliferation, migration, differentiation and survival. In addition, cells cultured under 3D conditions in presence of an ECM display a marked radioresistance towards ionizing radiation (IR) in comparison to conventionally 2D cultured cells. This process, also known as "cell-adhesion-mediated-radio-resistance" (CAM-RR), has been linked to the chromatin structure that differs between cells cultured on stiff surfaces versus cell grown on soft planar supports or in 3D environments. As integrins are the key mediators of cell adhesion and mechanosensing, they originate the molecular signalling towards chromatin remodelling in response to a cell's microenvironment. We aimed to investigate this molecular origin that leads to CAM-RR by investigating the distribution of integrins at the single molecule level and show that cells cultured in 2D keep a lower fraction of integrin β1 in clusters and maintain a less defined cluster status than 3D cultured cells. Upon X-irradiation this nanoscale distribution of integrin β1 is disturbed at much lower dosages in 2D versus 3D cultured cells. Radioresistance is thus linked to the ability to maintain a well defined organization of integrins in clusters, making integrin distribution a potential drug target for radiosensitization.
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Affiliation(s)
- Laura Babel
- Membrane Dynamics, Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany.,GRK 1657, Molecular and cellular responses to ionizing radiation, Technische Universität Darmstadt, Darmstadt, Germany
| | - Miriam Grunewald
- Membrane Dynamics, Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany.,GRK 1657, Molecular and cellular responses to ionizing radiation, Technische Universität Darmstadt, Darmstadt, Germany
| | - Robert Lehn
- Membrane Dynamics, Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Markus Langhans
- Membrane Dynamics, Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Tobias Meckel
- Membrane Dynamics, Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany. .,GRK 1657, Molecular and cellular responses to ionizing radiation, Technische Universität Darmstadt, Darmstadt, Germany.
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1748
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Szikora S, Földi I, Tóth K, Migh E, Vig A, Bugyi B, Maléth J, Hegyi P, Kaltenecker P, Sanchez-Soriano N, Mihály J. The formin DAAM is required for coordination of the actin and microtubule cytoskeleton in axonal growth cones. J Cell Sci 2017; 130:2506-2519. [PMID: 28606990 DOI: 10.1242/jcs.203455] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 06/05/2017] [Indexed: 01/10/2023] Open
Abstract
Directed axonal growth depends on correct coordination of the actin and microtubule cytoskeleton in the growth cone. However, despite the relatively large number of proteins implicated in actin-microtubule crosstalk, the mechanisms whereby actin polymerization is coupled to microtubule stabilization and advancement in the peripheral growth cone remained largely unclear. Here, we identified the formin Dishevelled-associated activator of morphogenesis (DAAM) as a novel factor playing a role in concerted regulation of actin and microtubule remodeling in Drosophilamelanogaster primary neurons. In vitro, DAAM binds to F-actin as well as to microtubules and has the ability to crosslink the two filament systems. Accordingly, DAAM associates with the neuronal cytoskeleton, and a significant fraction of DAAM accumulates at places where the actin filaments overlap with that of microtubules. Loss of DAAM affects growth cone and microtubule morphology, and several aspects of microtubule dynamics; and biochemical and cellular assays revealed a microtubule stabilization activity and binding to the microtubule tip protein EB1. Together, these data suggest that, besides operating as an actin assembly factor, DAAM is involved in linking actin remodeling in filopodia to microtubule stabilization during axonal growth.
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Affiliation(s)
- Szilárd Szikora
- Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, MTA-SZBK NAP B Axon Growth and Regeneration Group, Temesvári krt. 62, Szeged H-6726, Hungary
| | - István Földi
- Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, MTA-SZBK NAP B Axon Growth and Regeneration Group, Temesvári krt. 62, Szeged H-6726, Hungary
| | - Krisztina Tóth
- Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, MTA-SZBK NAP B Axon Growth and Regeneration Group, Temesvári krt. 62, Szeged H-6726, Hungary
| | - Ede Migh
- Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, MTA-SZBK NAP B Axon Growth and Regeneration Group, Temesvári krt. 62, Szeged H-6726, Hungary
| | - Andrea Vig
- University of Pécs, Medical School, Department of Biophysics, Szigeti str. 12, Pécs H-7624, Hungary
| | - Beáta Bugyi
- University of Pécs, Medical School, Department of Biophysics, Szigeti str. 12, Pécs H-7624, Hungary.,Szentágothai Research Center, Ifjúság str. 34, Pécs H-7624, Hungary
| | - József Maléth
- MTA-SZTE Translational Gastroenterology Research Group, First Department of Internal Medicine, Szeged H-6720, Hungary
| | - Péter Hegyi
- MTA-SZTE Translational Gastroenterology Research Group, First Department of Internal Medicine, Szeged H-6720, Hungary.,Institute for Translational Medicine, Department of Pathophysiology, University of Pécs, Pécs H-7624, Hungary
| | - Péter Kaltenecker
- Institute for Translational Medicine, Department of Cellular and Molecular Physiology, University of Liverpool, Liverpool L69 3BX, UK
| | - Natalia Sanchez-Soriano
- Institute for Translational Medicine, Department of Cellular and Molecular Physiology, University of Liverpool, Liverpool L69 3BX, UK
| | - József Mihály
- Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, MTA-SZBK NAP B Axon Growth and Regeneration Group, Temesvári krt. 62, Szeged H-6726, Hungary
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1749
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Shilts J, Broadie K. Secreted tissue inhibitor of matrix metalloproteinase restricts trans-synaptic signaling to coordinate synaptogenesis. J Cell Sci 2017; 130:2344-2358. [PMID: 28576972 DOI: 10.1242/jcs.200808] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 05/29/2017] [Indexed: 12/20/2022] Open
Abstract
Synaptogenesis is coordinated by trans-synaptic signals that traverse the specialized synaptomatrix between presynaptic and postsynaptic cells. Matrix metalloproteinase (Mmp) activity sculpts this environment, balanced by secreted tissue inhibitors of Mmp (Timp). Here, we use the simplified Drosophila melanogaster matrix metalloproteome to test the consequences of eliminating all Timp regulatory control of Mmp activity at the neuromuscular junction (NMJ). Using in situ zymography, we find Timp limits Mmp activity at the NMJ terminal and shapes extracellular proteolytic dynamics surrounding individual synaptic boutons. In newly generated timp null mutants, NMJs exhibit architectural overelaboration with supernumerary synaptic boutons. With cell-targeted RNAi and rescue studies, we find that postsynaptic Timp limits presynaptic architecture. Functionally, timp null mutants exhibit compromised synaptic vesicle cycling, with activity that is lower in amplitude and fidelity. NMJ defects manifest in impaired locomotor function. Mechanistically, we find that Timp limits BMP trans-synaptic signaling and the downstream synapse-to-nucleus signal transduction. Pharmacologically restoring Mmp inhibition in timp null mutants corrects bone morphogenetic protein (BMP) signaling and synaptic properties. Genetically restoring BMP signaling in timp null mutants corrects NMJ structure and motor function. Thus, Timp inhibition of Mmp proteolytic activity restricts BMP trans-synaptic signaling to coordinate synaptogenesis.
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Affiliation(s)
- Jarrod Shilts
- Department of Biological Sciences, Kennedy Center for Research on Human Development, Vanderbilt University, Nashville, TN 37235, USA
| | - Kendal Broadie
- Department of Biological Sciences, Kennedy Center for Research on Human Development, Vanderbilt University, Nashville, TN 37235, USA
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1750
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Tsuruta F, Okajima T, Yano S, Chiba T. Quantification of Endosome and Lysosome Motilities in Cultured Neurons Using Fluorescent Probes. J Vis Exp 2017. [PMID: 28570534 DOI: 10.3791/55488] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
In the brain, membrane trafficking systems play important roles in regulating neuronal functions, such as neuronal morphology, synaptic plasticity, survival, and glial communications. To date, numerous studies have reported that defects in these systems cause various neuronal diseases. Thus, understanding the mechanisms underlying vesicle dynamics may provide influential clues that could aid in the treatment of several neuronal disorders. Here, we describe a method for quantifying vesicle motilities, such as motility distance and rate of movement, using a software plug-in for the ImageJ platform. To obtain images for quantification, we labeled neuronal endosome-lysosome structures with EGFP-tagged vesicle marker proteins and observed the movement of vesicles using a time-lapse microscopy. This method is highly useful and simplify measuring vesicle motility in neurites, such as axons and dendrites, as well as in the soma of both neurons and glial cells. Furthermore, this method can be applied to other cell lines, such as fibroblasts and endothelial cells. This approach could provide a valuable advancement of our understanding of membrane trafficking.
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Affiliation(s)
- Fuminori Tsuruta
- Graduate School of Life and Environmental Sciences, University of Tsukuba; PhD Program in Human Biology, School of Integrative and Global Majors, University of Tsukuba; Life Science Center of Tsukuba Advanced Research Alliance (TARA), University of Tsukuba;
| | - Tomomi Okajima
- Graduate School of Life and Environmental Sciences, University of Tsukuba
| | - Sarasa Yano
- Graduate School of Life and Environmental Sciences, University of Tsukuba
| | - Tomoki Chiba
- Graduate School of Life and Environmental Sciences, University of Tsukuba; PhD Program in Human Biology, School of Integrative and Global Majors, University of Tsukuba; Life Science Center of Tsukuba Advanced Research Alliance (TARA), University of Tsukuba
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