Calcium Signalling: Methods and Protocols

252 Pages·2019·7.695 MB·English

by  Anna Raffaello, Denis Vecellio Reane

Methods in
Molecular Biology 1925
Anna Raff aello
Denis Vecellio Reane Editors
Calcium
Signalling
Methods and Protocols
M M B
ethods in olecular iology
Series Editor:
John M. Walker
School of Life and Medical Sciences
University of Hertfordshire
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Calcium Signalling
Methods and Protocols
Edited by
Anna Raffaello
Department of Biomedical Sciences, University of Padua, Padua, Italy
Denis Vecellio Reane
Department of Biomedical Sciences, University of Padua, Padua, Italy
Editors
Anna Raffaello Denis Vecellio Reane
Department of Biomedical Sciences Department of Biomedical Sciences
University of Padua University of Padua
Padua, Italy Padua, Italy
ISSN 1064-3745 ISSN 1940-6029 (electronic)
Methods in Molecular Biology
ISBN 978-1-4939-9017-7 ISBN 978-1-4939-9018-4 (eBook)
DOI 10.1007/978-1-4939-9018-4
Library of Congress Control Number: 2018966714
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Preface
The concept that calcium ions control physiological events goes back to 1883 when Ringer
observed that the addition of Ca2+ to the perfusion buffer of isolated hearts triggered their
contraction [1]. Many studies then allowed to clarify that the regulation of cytosolic cal-
cium concentrations ([Ca2+] ) relies on different sources: the extracellular medium, a vir-
cyt
tually unlimited reservoir of Ca2+, and intracellular pools (the most important intracellular
store is the endoplasmic reticulum (ER)) that allow rapid release through store-resident
channels [2]. The molecular nature of most of the channels responsible for Ca2+ entry
through the plasma membrane and mitochondria has been mysterious till about 10 years
ago and, only recently, the three-dimensional structure of the Ca2+-releasing channel of the
ER has been elucidated [3]. These seminal discoveries not only allowed the development of
genetic tools to modulate [Ca2+] in different organelles and the entry through the plasma
membrane but have been a potent stimulus to develop new strategies to develop new dyes
and genetically encoded probes to precisely estimate [Ca2+], avoiding artifacts due to differ-
ent pH and temperature conditions [3].
In this volume, leading researchers summarize the current state of the field from a
methodological standpoint. The present collection of novel methods is divided into 20
chapters, which cover a range of protocols for both in vitro and in vivo analyses in several
model systems. In detail, Chapters 1–4 cover the description of innovative methods to
measure [Ca2+] in different subcellular compartments using both genetically encoded and
Ca2+-sensitive dyes. Leading scientists in the field described methods to measure [Ca2+] in
plants (Chapter 8), parasites as Plasmodium falciparum (Chapter 14), and mammalian cells
such as skeletal muscle fibers (Chapters 9 and 10) and astrocytes (Chapter 16), just to name
a few. Furthermore, two chapters (6 and 7) describe methodologies to study single Ca2+
channels and purified channels, crucial to understand the properties of the channel and
their pharmacology.
It is widely accepted that Ca2+ ions control many cellular functions, ranging from
metabolism, muscle contraction, reactive oxygen species (ROS) production, and cell death
[2]. In this view, this volume describes also breakthrough methods to measure cellular pro-
cesses regulated by Ca2+. In detail, Chapter 17 describes methods to measure cellular ROS,
and Chapters 18–20 describe how to measure ATP and the functionality of the mitochon-
drial enzyme producing ATP, the ATP synthase.
During the preparation of this volume, we have been aided by the high quality input
from the large number of authors and we thank them all for their respective contributions.
This volume of Methods in Molecular Biology—Calcium Signalling is expected to
provide a comprehensive and reliable methodological guide from both a conceptual and
methodological standpoint to beginners and experts in this exciting and rapidly expanding
area of the study of calcium homeostasis research.
Padua, Italy Anna Raffaello
Denis Vecellio Reane
v
vi Preface
References
1. Ringer S (1883) A third contribution regarding the influence of the inorganic constitu-
ents of the blood on the ventricular contraction. J Physiol 4:222–5
2. Rizzuto R, et al (2012) Mitochondria as sensors and regulators of calcium signalling.
Nat Rev Mol Cell Biol 13:566–78
3. Raffaello A, et al (2016) Calcium at the center of cell signaling: interplay between endo-
plasmic reticulum, mitochondria, and lysosomes. Trends Biochem Sci 41
Acknowledgments
Anna Raffaello and Denis Vecellio Reane are supported by funding from the Italian Telethon
Foundation (GGP16026) and the French Muscular Dystrophy Association (AFM-Téléthon)
(19471).
vii
Contents
Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v
Acknowledgments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vii
Contributors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xi
1 High-Throughput Screening Using Photoluminescence Probe to Measure
Intracellular Calcium Levels . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
Simona Feno, Giulia Di Marco, Agnese De Mario, Halenya Monticelli,
and Denis Vecellio Reane
2 Exploiting Cameleon Probes to Investigate Organelles Ca2+ Handling . . . . . . . . . 15
Luisa Galla, Paola Pizzo, and Elisa Greotti
3 Measuring Ca2+ Levels in Subcellular Compartments with Genetically
Encoded GFP-Based Indicators . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
Mattia Vicario and Tito Calì
4 Methods to Measure Intracellular Ca2+ Concentration Using Ca2+-Sensitive
Dyes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
Sofia Zanin, Elisa Lidron, Rosario Rizzuto, and Giorgia Pallafacchina
5 MCU Regulation in Lipid Bilayer and Electrophysiological Recording . . . . . . . . . 59
Vanessa Checchetto and Ildikò Szabò
6 Electrophysiological Characterization of Calcium- Permeable Channels
Using Planar Lipid Bilayer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
Vanessa Checchetto and Ildikò Szabò
7 Patch-Clamp Analysis of the Mitochondrial Calcium Uniporter . . . . . . . . . . . . . . 75
Vivek Garg and Yuriy Y. Kirichok
8 In Vivo Light Sheet Fluorescence Microscopy of Calcium Oscillations
in Arabidopsis thaliana . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
Neli Romano Armada, Fabrizio Gandolfo Doccula, Alessia Candeo, Gianluca
Valentini, Alex Costa, and Andrea Bassi
9 Ex Vivo Measurements of Ca2+ Transients in Intracellular Compartments
of Skeletal Muscle Fibers by Means of Genetically Encoded Probes . . . . . . . . . . 103
Gaia Gherardi and Cristina Mammucari
10 Imaging Intracellular Ca2+ in Cardiomyocytes with Genetically Encoded
Fluorescent Probes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111
Antonio Campo and Marco Mongillo
11 In Vivo Monitoring of Ca2+ Uptake into Subcellular Compartments
of Mouse Skeletal Muscle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 127
Rüdiger Rudolf, Sofie Trajanovska, David Grant Allen, and Tullio Pozzan
12 TRPML1-/TFEB-Dependent Regulation of Lysosomal Exocytosis . . . . . . . . . . 143
Simone Di Paola and Diego L. Medina
ix
x Contents
13 Ca2+-Dependent Regulation of TFEB and Lysosomal Function . . . . . . . . . . . . . 145
Simone Di Paola and Diego L. Medina
14 Employing Transgenic Parasite Strains to Study the Ca2+ Dynamics
in the Human Malaria Parasite Plasmodium falciparum . . . . . . . . . . . . . . . . . . . 157
Lucas Borges-Pereira and Célia R. S. Garcia
15 Calcium Imaging of Store-Operated Calcium (Ca2+) Entry (SOCE)
in HEK293 Cells Using Fura-2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 163
Martin Johnson
16 Optogenetic Interneuron Stimulation and Calcium Imaging in Astrocytes . . . . . 173
Gabriele Losi, Anna Maria Lia, Marta Gomez-Gonzalo, Micaela Zonta, and
Giorgio Carmignoto
17 Measuring Calcium and ROS by Genetically Encoded Protein Sensors
and Fluorescent Dyes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 183
Christine S. Gibhardt, Adina Vultur, and Ivan Bogeski
18 Assessing Calcium-Stimulated Mitochondrial Bioenergetics Using the
Seahorse XF96 Analyzer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 197
Jennifer Wettmarshausen and Fabiana Perocchi
19 Determination of ATP, ADP, and AMP Levels by Reversed-Phase
High-Performance Liquid Chromatography in Cultured Cells . . . . . . . . . . . . . . 223
Michela Menegollo, Isabella Tessari, Luigi Bubacco, and Gyorgy Szabadkai
20 Purification of Functional F-ATP Synthase from Blue Native PAGE . . . . . . . . . . 233
Chiara Galber, Giulia Valente, Sophia von Stockum, and Valentina Giorgio
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .245