Methods in
Molecular Biology 2346
Kursad Turksen Editor
Stem Cell
Renewal
and Cell-Cell
Communication
Methods and Protocols
Second Edition
,METHODS IN MOLECULAR BIOLOGY
Series Editor
John M. Walker
School of Life and Medical Sciences
University of Hertfordshire
Hatfield, Hertfordshire, UK
For further volumes:
http://www.springer.com/series/7651
,For over 35 years, biological scientists have come to rely on the research protocols and
methodologies in the critically acclaimed Methods in Molecular Biology series. The series was
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constitute the key ingredient in each and every volume of the Methods in Molecular Biology
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,Stem Cell Renewal and Cell-Cell
Communication
Methods and Protocols
Second Edition
Edited by
Kursad Turksen
Ottawa, ON, Canada
,Editor
Kursad Turksen
Ottawa, ON, Canada
ISSN 1064-3745 ISSN 1940-6029 (electronic)
Methods in Molecular Biology
ISBN 978-1-0716-1569-0 ISBN 978-1-0716-1570-6 (eBook)
https://doi.org/10.1007/978-1-0716-1570-6
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,Preface
Great strides have been made in the field of cell–cell communications with respect to the
identification and characterization of key components of the communication apparatus,
assembly and maintenance of the communications structures, and concomitantly their
roles in not only tissue formation and maintenance but also regeneration and repair. In
this second edition of the Stem Cell Renewal and Cell-Cell Communication volume, I have
brought together a new set of protocols to arm cell biologists with protocols that are
currently being used in a number of well-established laboratories around the world. I
hope that both people already in the field as well as newcomers will benefit from this
compilation, and that the volume will drive continued growth in our understanding of the
crucial biological and physiological roles of cell–cell communications in tissue function and
organismal integrity.
Once again, the protocols gathered here are faithful to the mission statement of the
Methods in Molecular Biology series: They are well-established and described in an easy to
follow, step-by-step fashion so as to be valuable for not only experts but also novices in the
field. That goal is achieved because of the generosity of the contributors who have carefully
described their protocols in this volume, and I am very grateful for their efforts.
My thanks as well go to Dr. John Walker, the Editor-in-Chief of the Methods in
Molecular Biology series, for giving me the opportunity to create this volume and for
supporting me along the way.
I am also grateful to Patrick Marton, the Executive Editor of Methods in Molecular
Biology and the Springer Protocols collection, for his continuous support from idea to
completion of this volume.
A special thank you goes to Anna Rakovsky, Assistant Editor for Methods in Molecular
Biology, for her continuous support from beginning to end of this project.
I would also like to thank David C. Casey, Senior Editor of Methods in Molecular Biology,
for his outstanding editorial work during the production of this volume.
Finally, I would like to thank Anand Ventakachalam and the rest of the production crew
for their work in putting together an outstanding volume.
Ottawa, ON, Canada Kursad Turksen
v
,Contents
Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v
Contributors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix
Inference of Ligand–Receptor Pairs from Single-Cell Transcriptomics Data. . . . . . . . . 1
Mirjana Efremova and Roser Vento-Tormo
Multiple Imaging Modalities for Cell-Cell Communication via Calcium
Mobilizations in Corneal Epithelial Cells . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Yoonjoo K. Lee, Kristen L. Segars, and Vickery Trinkaus-Randall
Interactions of Hematopoietic Stem Cells with Bone Marrow Niche. . . . . . . . . . . . . . . 21
Xinghui Zhao, Cuiping Zhang, Xiaojing Cui, and Ying Liang
Ex Vivo Modeling of Hematopoietic Stem Cell Homing to the Fetal Liver . . . . . . . . . 35
Amina Mohammadalipour, Miguel F. Diaz, Sumedha Pareek,
and Pamela L. Wenzel
Analysis of Epithelial Architecture and Planar Spindle Orientation
in the Drosophila Wing Disc. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
Yu-ichiro Nakajima
A Co-culture Model to Study the Effect of Kidney Fibroblast-p90RSK
on Epithelial Cell Survival . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
Ling Lin, Samantha White, and Kebin Hu
Calcium Fluorescence Recordings from Neuroepithelial Stem Cells. . . . . . . . . . . . . . . . 73
Masayuki Yamashita
Ultrastructural Analysis of Cell–Cell Interactions in Drosophila Ovary . . . . . . . . . . . . . 79
Matthew Antel, Valentina Baena, Mark Terasaki, and Mayu Inaba
TIRF Microscopy as a Tool to Determine Exosome Composition . . . . . . . . . . . . . . . . . 91
Noa B. Martı́n-Co freces, Daniel Torralba, Marta Lozano-Prieto,
Nieves Fernández-Gallego, and Francisco Sánchez-Madrid
Rapid Visualization of Intracellular Vesicle Events During Synaptic
Stimulation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105
Noa B. Martı́n-Co freces, Amelia Rojas-Gomez, Sara G. Dosil,
Irene Fernandez-Delgado, and Francisco Sánchez-Madrid
Monitoring of Active Notch Signaling in Mouse Bladder Urothelium . . . . . . . . . . . . . 121
Panagiotis Karakaidos and Theodoros Rampias
Examining Local Cell-to-Cell Signalling in the Kidney Using ATP Biosensing . . . . . . 135
Gareth W. Price, Joe A. Potter, Bethany M. Williams, Chelsy L. Cliff,
Mark J. Wall, Claire E. Hills, and Paul E. Squires
Isolation and Assessment of Pancreatic Islets Versus Dispersed Beta Cells:
A Straightforward Approach to Examine Cell–Cell Communication . . . . . . . . . . . . . . . 151
Rachel T. Scarl, William J. Koch, Kathryn L. Corbin, and Craig S. Nunemaker
vii
,viii Contents
Promoter Pull-Down Assay: A Biochemical Screen for DNA-Binding
Proteins . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 165
Ryan R. Chaparian and Julia C. van Kessel
Purification of the Vibrio Quorum-Sensing Transcription Factors LuxR,
HapR, and SmcR. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 173
Jane D. Newman and Julia C. van Kessel
Preserving Cytonemes for Immunocytochemistry of Cultured Adherent
Cells . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 183
Sally Rogers and Steffen Scholpp
Fluorescent Labeling of Connexin with As Complex and X-Y Coordinate
Registration of Target Single Cells Based on a Triangle Standard Chip
for the Image Analysis of Gap Junctional Communication. . . . . . . . . . . . . . . . . . . . . . . . 191
Mikako Saito
Chemical and Voltage Gating of Gap Junction Channels Expressed
in Xenopus Oocytes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 207
Camillo Peracchia
The Analysis of Gap Junctional Intercellular Communication Among
Osteocytes in Chick Calvariae by Fluorescence Recovery After Photobleaching . . . . . 215
Ziyi Wang, Yoshihito Ishihara, and Hiroshi Kamioka
Flow Cytometry Evaluation of Gap Junction-Mediated Intercellular
Communication Between Cytotoxic T Cells and Target Tumor Cells . . . . . . . . . . . . . . 225
Mariela Navarrete, Flavio Salazar-Onfray, and Andrés Tittarelli
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 237
,Contributors
MATTHEW ANTEL • Department of Cell Biology, University of Connecticut Health Center,
Farmington, CT, USA
VALENTINA BAENA • Department of Cell Biology, University of Connecticut Health Center,
Farmington, CT, USA
RYAN R. CHAPARIAN • Biology Department, Indiana University, Bloomington, IN, USA
CHELSY L. CLIFF • Joseph Banks Laboratories, School of Life Sciences, University of Lincoln,
Lincoln, UK
KATHRYN L. CORBIN • Department of Biomedical Sciences Heritage College of Osteopathic
Medicine, Ohio University, Athens, OH, USA; Diabetes Institute, Heritage College of
Osteopathic Medicine, Ohio University, Athens, OH, USA
XIAOJING CUI • Department of Toxicology and Cancer Biology, University of Kentucky,
Lexington, KY, USA
MIGUEL F. DIAZ • Department of Integrative Biology and Pharmacology, McGovern Medical
School, University of Texas Health Science Center at Houston, Houston, TX, USA; Center
for Stem Cell and Regenerative Medicine, The Brown Foundation Institute of Molecular
Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA
SARA G. DOSIL • Servicio de Inmunologı́a, Hospital Universitario de la Princesa,
Universidad Autonoma de Madrid, Instituto Investigacion Sanitaria Princesa (IIS-IP),
Madrid, Spain; Vascular Pathophysiology Area, Centro Nacional Investigaciones
Cardiovasculares (CNIC), Madrid, Spain
MIRJANA EFREMOVA • Barts Cancer Institute, Queen Mary University of London, London,
UK; Wellcome Sanger Institute, Cambridgeshire, UK
IRENE FERNANDEZ-DELGADO • Servicio de Inmunologı́a, Hospital Universitario de la
Princesa, Universidad Autonoma de Madrid, Instituto Investigacion Sanitaria Princesa
(IIS-IP), Madrid, Spain; Vascular Pathophysiology Area, Centro Nacional Investigaciones
Cardiovasculares (CNIC), Madrid, Spain
NIEVES FERNÁNDEZ-GALLEGO • Servicio de Inmunologı́a, Hospital Universitario de la
Princesa, Universidad Autonoma de Madrid, Instituto Investigacion Sanitaria Princesa
(IIS-IP), Madrid, Spain; Vascular Pathophysiology Area, Centro Nacional Investigaciones
Cardiovasculares (CNIC), Madrid, Spain
CLAIRE E. HILLS • Joseph Banks Laboratories, School of Life Sciences, University of Lincoln,
Lincoln, UK
KEBIN HU • Department of Medicine, The Pennsylvania State University College of
Medicine, Hershey, PA, USA; Department of Cellular and Molecular Physiology, The
Pennsylvania State University College of Medicine, Hershey, PA, USA
MAYU INABA • Department of Cell Biology, University of Connecticut Health Center,
Farmington, CT, USA
YOSHIHITO ISHIHARA • Department of Orthodontics, Okayama University Graduate School of
Medicine, Dentistry, and Pharmaceutical Sciences, Okayama, Japan
HIROSHI KAMIOKA • Department of Orthodontics, Okayama University Graduate School of
Medicine, Dentistry, and Pharmaceutical Sciences, Okayama, Japan
PANAGIOTIS KARAKAIDOS • Biomedical Research Foundation of the Academy of Athens,
Athens, Greece
ix
, x Contributors
WILLIAM J. KOCH • Department of Biomedical Sciences Heritage College of Osteopathic
Medicine, Ohio University, Athens, OH, USA; Translational Biomedical Sciences,
Heritage College of Osteopathic Medicine, Ohio University, Athens, OH, USA; Diabetes
Institute, Heritage College of Osteopathic Medicine, Ohio University, Athens, OH, USA
YOONJOO K. LEE • Departments of Pharmacology and Biochemistry, Boston University School
of Medicine, Boston, MA, USA
YING LIANG • Department of Toxicology and Cancer Biology, University of Kentucky,
Lexington, KY, USA
LING LIN • Department of Medicine, The Pennsylvania State University College of Medicine,
Hershey, PA, USA; Department of Cellular and Molecular Physiology, The Pennsylvania
State University College of Medicine, Hershey, PA, USA
MARTA LOZANO-PRIETO • Servicio de Inmunologı́a, Hospital Universitario de la Princesa,
Universidad Autonoma de Madrid, Instituto Investigacion Sanitaria Princesa (IIS-IP),
Madrid, Spain; Vascular Pathophysiology Area, Centro Nacional Investigaciones
Cardiovasculares (CNIC), Madrid, Spain
NOA B. MARTÍN-CÓFRECES • Servicio de Inmunologı́a, Hospital Universitario de la Princesa,
Universidad Autonoma de Madrid, Instituto Investigacion Sanitaria Princesa (IIS-IP),
Madrid, Spain; Vascular Pathophysiology Area, Centro Nacional Investigaciones
Cardiovasculares (CNIC), Madrid, Spain; Centro de Investigacion Biomédica en Red
Cardiovascular (CIBERCV), Madrid, Spain
AMINA MOHAMMADALIPOUR • Department of Integrative Biology and Pharmacology,
McGovern Medical School, University of Texas Health Science Center at Houston, Houston,
TX, USA
YU-ICHIRO NAKAJIMA • Frontier Research Institute for Interdisciplinary Sciences, Tohoku
University, Sendai, Japan; Graduate School of Life Sciences, Tohoku University, Sendai,
Japan
MARIELA NAVARRETE • Millennium Institute on Immunology and Immunotherapy, Faculty
of Medicine, Universidad de Chile, Santiago, Chile; Disciplinary Program of Immunology,
Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago,
Chile
JANE D. NEWMAN • Biology Department, Indiana University, Bloomington, IN, USA
CRAIG S. NUNEMAKER • Department of Biomedical Sciences Heritage College of Osteopathic
Medicine, Ohio University, Athens, OH, USA; Diabetes Institute, Heritage College of
Osteopathic Medicine, Ohio University, Athens, OH, USA
SUMEDHA PAREEK • Immunology Program, MD Anderson Cancer Center UTHealth
Graduate School of Biomedical Sciences, Houston, TX, USA
CAMILLO PERACCHIA • Department of Pharmacology and Physiology, School of Medicine and
Dentistry, University of Rochester, Rochester, NY, USA
JOE A. POTTER • Joseph Banks Laboratories, School of Life Sciences, University of Lincoln,
Lincoln, UK
GARETH W. PRICE • Joseph Banks Laboratories, School of Life Sciences, University of Lincoln,
Lincoln, UK
THEODOROS RAMPIAS • Biomedical Research Foundation of the Academy of Athens, Athens,
Greece
SALLY ROGERS • Living Systems Institute, School of Biosciences, College of Life and
Environmental Sciences, University of Exeter, Exeter, UK
AMELIA ROJAS-GOMEZ • Servicio de Inmunologı́a, Hospital Universitario de la Princesa,
Universidad Autonoma de Madrid, Instituto Investigacion Sanitaria Princesa (IIS-IP),
