Synapse Development: Methods and Protocols

366 Pages·2017·16.32 MB·English

by  Alexandros Poulopoulos (eds.)

Methods in
Molecular Biology 1538
Alexandros Poulopoulos Editor
Synapse
Development
Methods and Protocols
M M B
ETHODS IN OLECULAR IOLOGY
Series Editor
John M. Walker
School of Life and Medical Sciences
University of Hertfordshire
Hatfield, Hertfordshire, AL10 9AB , UK
For further volumes:
http://www.springer.com/series/7651
Synapse Development
Methods and Protocols
Edited by
Alexandros Poulopoulos
Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
Editor
Alexandros Poulopoulos
Department of Stem Cell and Regenerative Biology
Harvard University
Cambridge, MA, USA
ISSN 1064-3745 ISSN 1940-6029 (electronic)
Methods in Molecular Biology
ISBN 978-1-4939-6686-8 ISBN 978-1-4939-6688-2 (eBook)
DOI 10.1007/978-1-4939-6688-2
Library of Congress Control Number: 2016956874
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Prefa ce
This book is a collection of protocols for experimentation into how neurons connect to
produce the extraordinary functionalities of the nervous system. The complexity underly-
ing the development of synapses allows and warrants an assortment of approaches to probe
the many layers of structure, mechanism, and emergent function. Appropriately, neurosci-
ence is populated by researchers across disciplines, and with them comes a range of tech-
nologies and methodologies that make the neuroscience toolkit one of characteristic wealth.
The experimental diversity converging onto the synapse has made it one of the most
intensely studied and intricately described biological systems. Observing in real-time how a
single protein fl ips between conformational states to regulate ion fl ows, following how thin
cellular protrusions traverse the body to form networks of the highest complexity seen in
nature, measuring how circuits interact and morph throughout the span of life to docu-
ment its story, our understanding of synapse development is arguably unparalleled in its
pluralism of perspective. Yet it seems the more detailed our descriptions, the more expan-
sive their heterogeneity and the less inclusive the models. Depending on the system in ques-
tion, synaptogenic behaviors range anywhere from the preordained pairings of Sperrian
chemoaffi nity to the play-by-ear modes of promiscuous exuberance and subsequent refi ne-
ment. Plasticity in turn occurs up or down, fl eeting or perduring, and is stirred on by mol-
ecules, voltages, and timing. While thankfully all these serve to construct a system able to
produce both hiccups and quantum theory, they also do away with comfy notions of a
generalizable synapse awaiting full description. The challenge is on, and the design of clever
new experimentation ever more opportune.
In putting together this volume, we’ve had the aim of compiling a laboratory guide
that covers a broad spectrum of applicable methods (largely excluding electrophysiology ,
which has merited its own dedicated volumes in this series), with the benefi t of a narrower
focus of implementation to the study of synapse development. I’ve asked experts to present
the current state of the art of classic protocols, giving their insider tweaks, tips, and tricks
for optimal application to the synapse and its particularities. I’ve also asked pioneers of
highly specialized approaches to contribute detailed guides to methods utilizing sophisti-
cated instrumentation that is often institutionally available to labs but for which method-
ological expertise is diffi cult to come by. These 23 chapters by 63 investigators are presented
in fi ve parts that deal with synapses: (1) in culture, (2) their constituents, (3) their struc-
tures, (4) their dynamics, and (5) the assemblies they form. Our hope is that these guides
will minimize the barrier to entry for the integration of new approaches with existing exper-
tise, producing syntheses that will foster novel perspectives on the many ways in which
synapses form, transform, and transmit.
Cambridge, MA, USA Alexandros Poulopoulos
v
Contents
Preface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v
Contributors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . i x
PART I FORMING SYNAPSES IN A DISH
1 A Cell Culture System to Investigate the Presynaptic Control
of Subsynaptic Membrane Differentiation at the Neuromuscular Junction. . . . 3
Nadine Schmidt , S reya Basu , S tephan Kröger , and Hans Rudolf Brenner
2 C o-culture Synaptogenic Assay: A New Look at Fluorescence Reporters
and Technological Devices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 3
Karen Perez de Arce and Massimiliano Stagi
3 S ynaptogenic Assays Using Neurons Cultured
on Micropatterned Substrates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 9
Katalin Czöndör and Olivier Thoumine
4 M onitoring Synapses Via Trans-Synaptic GFP Complementation. . . . . . . . . . . 4 5
Theodoros Tsetsenis
5 G eneration of Spinal Motor Neurons from Human Pluripotent
Stem Cells. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
David P. Santos and Evangelos Kiskinis
PART II ANALYZING SYNAPTIC CONSTITUENTS
6 B iochemical Purification of Binding Partners of Synaptic Scaffold Proteins . . . 6 9
Bekir Altas , O laf Jahn , and Hiroshi Kawabe
7 I n Situ Protein Binding Assay Using Fc-Fusion Proteins . . . . . . . . . . . . . . . . . 8 3
Nirmala Padmanabhan and Tabrez J. Siddiqui
8 R econstitution of Synaptic SNAREs into Large Liposomes
with Reduced Curvature Stress . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 3
Javier M. Hernandez
9 I solation of Synaptosomes, Synaptic Plasma Membranes,
and Synaptic Junctional Complexes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107
Mary L. Michaelis , L ei Jiang , and Elias K. Michaelis
10 P urification of Synaptosome Populations Using Fluorescence-Activated
Synaptosome Sorting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 121
Elisa Luquet , C hristoph Biesemann , A nnie Munier , and Etienne Herzog
PART III OBSERVING SYNAPTIC STRUCTURE AND ULTRASTRUCTURE
11 O ptimized Protocol for Imaging Cleared Neural Tissues
Using Light Microscopy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 37
Yoh Isogai , D ouglas S. Richardson , C atherine Dulac , and Joseph Bergan
vii
viii Contents
12 S tructured Illumination Microscopy for the Investigation
of Synaptic Structure and Function. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 155
Soyon Hong , D aniel K. Wilton , B eth Stevens , and Douglas S. Richardson
13 3 D d STORM Imaging of Fixed Brain Tissue . . . . . . . . . . . . . . . . . . . . . . . . . 1 69
Frank Herrmannsdörfer , B enjamin Flottmann , S iddarth Nanguneri ,
Varun Venkataramani , H einz Horstmann , T homas Kuner ,
and Mike Heilemann
14 P hotomarking Relocalization Technique for Correlated Two-Photon
and Electron Microcopy Imaging of Single Stimulated Synapses . . . . . . . . . . . 1 85
Miquel Bosch , J orge Castro , M riganka Sur , and Yasunori Hayashi
15 3 D Analysis of Synaptic Ultrastructure in Organotypic Hippocampal Slice
Culture by High-Pressure Freezing and Electron Tomography . . . . . . . . . . . . 215
Cordelia I mig and Benjamin H. Cooper
PART IV FOLLOWING SYNAPSE DYNAMICS
16 A nalyzing Endosomal Docking, Fusion, Sorting, and Budding
Mechanisms in Isolated Organelles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 235
Sina V. Barysch and Ioanna Bethani
17 C oncurrent Imaging of Receptor Trafficking and Calcium Dynamics
by Spinning Disk Confocal Microscopy. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 249
DeLaine D. Larsen , R egina Wai-Yan Choy , and Minjong Park
18 I maging Activity-Dependent Signaling Dynamics at the Neuronal Synapse
Using FRET-Based Biosensors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 61
Zohreh Farsi and Andrew Woehler
19 A nalyzing Structural Plasticity of Dendritic Spines in Organotypic
Slice Culture. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 277
Mathias De Roo and Adema Ribic
PART V REVEALING PATTERNS OF SYNAPTIC CONNECTIVITY
20 U sing Fluorescent Markers to Estimate Synaptic Connectivity In Situ . . . . . . . 293
Mrinalini Hoon , R aunak Sinha , and Haruhisa Okawa
21 D ual Anterograde and Retrograde Viral Tracing of Reciprocal Connectivity . . . . 3 21
Matthias G. Haberl , M elanie Ginger , and Andreas Frick
22 M apping Synaptic Inputs of Developing Neurons Using Calcium Imaging . . . . . 3 41
Johan Winnubst and Christian Lohmann
23 M onosynaptic Tracing in Developing Circuits Using Modified Rabies Virus . . . . 3 53
Laura Cocas and Gloria Fernandez
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 67
Contributors
BEKIR ALTAS • Department of Molecular Neurobiology, M ax Planck Institute
of Experimental Medicine , G öttingen, G ermany
SINA V. BARYSCH • Zentrum für Molekulare Biologie Heidelberg (ZMBH), DKFZ-Z MBH
Alliance , H eidelberg, G ermany
SREYA BASU • Department of Cell Biology and Genetics, E rasmus MC , R otterdam ,
The Netherlands
JOSEPH BERGAN • Department of Psychological and Brain Sciences, U niversity
of Massachusetts , A mherst , M A, U SA
IOANNA BETHANI • Department of Neurobiology, M ax Planck Institute for Biophysical
Chemistry , G öttingen, G ermany
CHRISTOPH BIESEMANN • Department of Molecular Neurobiology, M ax Planck Institute
of Experimental Medicine , G öttingen, G ermany
MIQUEL BOSCH • Institute for Bioengineering of Catalonia (IBEC) , B arcelona, S pain
HANS RUDOLF BRENNER • Department of Biomedicine, U niversity of Basel , B asel,
Switzerland
JORGE CASTRO • Department of Brain and Cognitive Sciences, The Picower Institute
for Learning and Memory , M assachusetts Institute of Technology , C ambridge, M A, U SA
REGINA WAI-YAN CHOY • Department of Psychiatry, School of Medicine, U niversity of
California , S an Francisco, C A , U SA
LAURA COCAS • Department of Neurology, University of California , San Francisco, CA , USA
BENJAMIN H. COOPER • Department of Molecular Neurobiology, M ax Planck Institute
of Experimental Medicine , G öttingen, G ermany
KATALIN CZÖNDÖR • Interdisciplinary Institute for Neuroscience , U niversity of Bordeaux
and CNRS , B ordeaux, F rance ; Interdisciplinary Institute for Neuroscience, CNRS,
UMR 5297, Bordeaux, France
MATHIAS DE ROO • Department of Neuroscience, School of Medicine , U niversity of Geneva ,
Geneva, S witzerland
CATHERINE DULAC • Department of Molecular and Cellular Biology, Howard Hughes
Medical Institute, H arvard University , C ambridge, M A, U SA
ZOHREH FARSI • Department of Neurobiology, M ax Planck Institute for Biophysical
Chemistry , G öttingen, G ermany
GLORIA FERNANDEZ • Department of Biological Sciences, C alifornia State University ,
Los Angeles, C A , U SA
BENJAMIN FLOTTMANN • Institute of Physical and Theoretical Chemistry , G oethe-U niversity
Frankfurt , F rankfurt, G ermany
ANDREAS FRICK • Neurocentre Magendie, I NSERM , B ordeaux, F rance ; U niversity of Bordeaux ,
Bordeaux, F rance
MELANIE GINGER • Neurocentre Magendie , I NSERM , B ordeaux, F rance ; U niversity
of Bordeaux , B ordeaux, F rance
ix
x Contributors
MATTHIAS G. HABERL • Neurocentre Magendie , I NSERM , B ordeaux, F rance ; U niversity
of Bordeaux , B ordeaux, F rance
YASUNORI HAYASHI • Brain Science Institute, RIKEN , W ako , J apan
MIKE HEILEMANN • Institute of Physical and Theoretical Chemistry , G oethe-University
Frankfurt , F rankfurt, G ermany
JAVIER M. HERNANDEZ • Department of Structural Biochemistry, Max Planck Institute for
Molecular Physiology, Dortmund, Germany
FRANK HERRMANNSDÖRFER • Department of Functional Neuroanatomy, H eidelberg
University , H eidelberg, G ermany
ETIENNE HERZOG • Interdisciplinary Institute for Neuroscience , U niversity of Bordeaux ,
Bordeaux, F rance ; I nterdisciplinary Institute for NeuroScience, CNRS , B ordeaux,
France
SOYON HONG • Department of Neurology, F.M. Kirby Neurobiology Center , B oston
Children’s Hospital, Harvard Medical School , B oston , M A, U SA ; Program in
Neuroscience, Harvard Medical School, Boston, MA, USA
MRINALINI HOON • Department of Biological Structure, U niversity of Washington , S eattle ,
WA, U SA
HEINZ HORSTMANN • Department of Functional Neuroanatomy, H eidelberg University ,
Heidelberg, G ermany
CORDELIA IMIG • Department of Molecular Neurobiology, M ax Planck Institute
of Experimental Medicine , G öttingen, G ermany
YOH ISOGAI • Department of Molecular and Cellular Biology, Howard Hughes Medical
Institute, Harvard University, Cambridge, MA, USA; Sainsbury Wellcome Centre for
Neural Circuits and Behaviour , U niversity College London , L ondon , U K
OLAF JAHN • Proteomics Group , M ax Planck Institute of Experimental Medicine ,
Göttingen, G ermany
LEI JIANG • Higuchi Biosciences Center, U niversity of Kansas , L awrence, K S , U SA
HIROSHI KAWABE • Department of Molecular Neurobiology, M ax Planck Institute
of Experimental Medicine , G öttingen, G ermany
EVANGELOS KISKINIS • The Ken & Ruth Davee Department of Neurology & Clinical
Neurological Sciences, Department of Physiology, Feinberg School
of Medicine, N orthwestern University , C hicago, I L, U SA
STEPHAN KÖGER • Department of Physiological Genomics, L udwig Maximilians University ,
Munich, G ermany
THOMAS KUNER • Department of Functional Neuroanatomy, H eidelberg University ,
Heidelberg, G ermany
DELAINE D. LARSEN • Department of Biochemistry and Biophysics, School of Medicine,
University of California , S an Francisco, C A , U SA
CHRISTIAN LOHMANN • Department of Synapse and Network Development, N etherlands
Institute for Neuroscience , A msterdam, T he Netherlands
ELISA LUQUET • Interdisciplinary Institute for Neuroscience , U niversity of Bordeaux ,
Bordeaux, F rance ; I nterdisciplinary Institute for NeuroScience, CNRS , B ordeaux,
France
ELIAS K. MICHAELIS • Higuchi Biosciences Center, University of Kansas , Lawrence, KS , USA
MARY L. MICHAELIS • Higuchi Biosciences Center, University of Kansas , Lawrence, KS , USA
ANNIE MUNIER • Institut de Biologie Paris Seine, U niversity Pierre et Marie Curie , P aris ,
France
SIDDARTH NANGUNERI • Department of Functional Neuroanatomy, H eidelberg University ,
Heidelberg, G ermany
Contributors xi
HARUHISA OKAWA • Department of Biological Structure, U niversity of Washington , S eattle ,
WA, U SA
NIRMALA PADMANABHAN • Department of Physiology and Pathophysiology, Max Rady
College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg ,
MB, C anada ; N euroscience Research Program, Kleysen Institute for Advanced Medicine,
Health Sciences Centre, University of Manitoba , W innipeg, M B, C anada
MINJONG PARK • Department of Psychiatry, School of Medicine, U niversity of California ,
San Francisco, C A , U SA
KAREN PEREZ DE ARCE • Department of Neuroscience, School of Medicine , T ufts University ,
Boston , M A, U SA
ADEMA RIBIC • Department of Neuroscience, School of Medicine , T ufts University , B oston ,
MA, U SA
DOUGLAS S. RICHARDSON • Department of Molecular and Cellular Biology, Harvard
University, Cambridge, MA, USA; Harvard Center for Biological Imaging, Harvard
University, Cambridge, MA, USA
DAVID P. SANTOS • The Ken & Ruth Davee Department of Neurology & Clinical
Neurological Sciences, Department of Physiology, Feinberg School of Medicine,
Northwestern University , C hicago, I L, U SA
NADINE SCHMIDT • Department of Physiology II, A lbert-Ludwigs University , F reiburg,
Germany
TABREZ J. SIDDIQUI • Department of Physiology and Pathophysiology, Max Rady College of
Medicine, Rady Faculty of Health Sciences ; U niversity of Manitoba , W innipeg, M B,
Canada ; Neuroscience Research Program, Kleysen Institute for Advanced Medicine,
Health Sciences Centre, University of Manitoba, Winnipeg, MB
RAUNAK SINHA • Department of Physiology and Biophysics, U niversity of Washington ,
Seattle , W A, U SA
MASSIMILIANO STAGI • Department of Cellular and Molecular Physiology, Institute
of Translational Medicine, U niversity of Liverpool , L iverpool, U K ; University of
Liverpool, Crown Street, Liverpool, UK
BETH STEVENS • Department of Neurology, F.M. Kirby Neurobiology Center ,
Boston Children’s Hospital, Harvard Medical School , B oston , M A, U SA ;
Program in Neuroscience, Harvard Medical School, Boston, MA, USA
MRIGANKA SUR • Department of Brain and Cognitive Sciences, The Picower Institute
for Learning and Memory , M assachusetts Institute of Technology , C ambridge, M A, U SA
OLIVIER THOUMINE • Interdisciplinary Institute for Neuroscience , U niversity of Bordeaux ,
Bordeaux, F rance ; C NRS , B ordeaux, F rance ; Interdisciplinary Institute for
Neuroscience, CNRS, UMR 5297, Bordeaux, France
THEODOROS TSETSENIS • Department of Neuroscience, Mahoney Institute for Neurosciences,
Perelman School for Medicine, U niversity of Pennsylvania , P hiladelphia, P A, U SA
VARUN VENKATARAMANI • Department of Functional Neuroanatomy, Heidelberg University ,
Heidelberg, G ermany
DANIEL K. WILTON • Department of Neurology, F.M. Kirby Neurobiology Center , B oston
Children’s Hospital, Harvard Medical School , B oston , M A, U SA ; Program in
Neuroscience, Harvard Medical School, Boston, MA, USA
JOHAN WINNUBST • Janelia Research Campus, H oward Hughes Medical Institute , A shburn,
VA, U SA
ANDREW WOEHLER • Berlin Institute for Medical Systems Biology, M ax Delbrueck Center
for Molecular Medicine in the Helmholtz Association , B erlin-Buch, G ermany