Stress Responses: Methods and Protocols

248 Pages·2015·8.044 MB·English

by  Christine M. Oslowski (eds.)

Methods in
Molecular Biology 1292
Christine M. Oslowski Editor
Stress
Responses
Methods and Protocols
M M B
ETHODS IN OLECULAR IOLOGY
Series Editor
John M. Walker
School of Life and Medical Sciences
University of Hertfordshire
Hat fi eld, Hertfordshire, AL10 9AB, UK
For further volumes:
http://www.springer.com/series/7651

Stress Responses
Methods and Protocols
Edited by
Christine M. Oslowski
Wentworth Institute of Technology, Boston, MA, USA
Editor
Christine M . Oslowski
Wentworth Institute of Technology
Boston, MA , USA
ISSN 1064-3745 ISSN 1940-6029 (electronic)
Methods in Molecular Biology
ISBN 978-1-4939-2521-6 ISBN 978-1-4939-2522-3 (eBook)
DOI 10.1007/978-1-4939-2522-3
Library of Congress Control Number: 2015934151
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Prefa ce
Cells are bombarded by stresses on a regular basis. Luckily, cells are armed with several
mechanisms to mitigate cell stress and promote cell survival. However, under severe stress
conditions, cells undergo dysfunction and ultimately death. This volume of Methods in
Molecular Biology includes an array of protocols to detect and study the different cellular
stresses, measure their pathological consequences within the cell, and investigate the role of
cellular stresses in select diseases. Understanding the mechanisms of the multiple cellular
pathways and outcomes triggered by such stresses will lead to the development of novel
therapeutics to prevent or treat disease. At the conclusion of this volume, reviews on the
crosstalk between different pathways, stress responses during ageing, and targeting stress
are included.
Boston, MA, USA Christine M. Oslowski
v

Contents
Preface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v
Contributors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . i x
PART I A SSAYS FOR DETECTING AND CHARACTERIZING A VARIETY
OF CELLULAR PROCESSES UNDER CELL STRESS
1 M ethods for Studying ER Stress and UPR Markers in Human Cells . . . . . . . . 3
Donna Kennedy , A fshin Samali , and Richard Jäger
2 A ssays for Induction of the Unfolded Protein Response and Selective
Activation of the Three Major Pathways . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
Ananya Gupta , D anielle E. Read , and Sanjeev Gupta
3 A ssays to Characterize Molecular Chaperone Function In Vitro. . . . . . . . . . . . 3 9
Martin Haslbeck and Johannes Buchner
4 A nalysis of the Heat Shock Factor Complex in Mammalian
HSP70 Promoter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 3
Mitsuaki Fujimoto , R yosuke Takii , N aoki Hayashida , and Akira Nakai
5 I mmunofluorescence-Based Methods to Monitor DNA End Resection. . . . . . 6 7
Bipasha Mukherjee , N ozomi Tomimatsu , and Sandeep Burma
6 V isualizing the Spatiotemporal Dynamics of DNA Damage
in Budding Yeast. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77
Chihiro Horigome , V incent Dion , A ndrew Seeber , L utz R. Gehlen ,
and S usan M. Gasser
7 D etecting Reactive Oxygen Species by Immunohistochemistry . . . . . . . . . . . . 9 7
Geou-Yarh Liou and Peter Storz
8 I nvestigating Inflammasome Activation Under Conditions
of Cellular Stress and Injury . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105
Clare C. Cunningham , E mma M. Corr , D onal J. Cox , and Aisling Dunne
9 M ethods for Studying microRNA Functions During Stress . . . . . . . . . . . . . . . 1 15
Yoshinari Ando and Anthony K. L. Leung
10 M easuring Autophagy in Stressed Cells. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 129
Marina N. Sharifi , E rin E. Mowers , L auren E. Drake ,
and K ay F. Macleod
11 D etection of Apoptosis Using Fluorescent Probes. . . . . . . . . . . . . . . . . . . . . . 1 51
Grishma Khanal , H imali Somaweera , M eicong Dong , T odd Germain ,
Megan Ansari , and Dimitri Pappas
PART II STUDYING CELL STRESS IN THE CONTEXT OF DISEASE
12 M easuring Death of Pancreatic Beta Cells in Response to Stress
and Cytotoxic T Cells. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 165
Jibran A. Wali , P rerak Trivedi , T homas W. Kay , and Helen E. Thomas
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viii Contents
13 A daptation of the Secretory Pathway in Cancer Through IRE1 Signaling . . . . 1 77
Stéphanie Lhomond , N estor Pallares , K im Barroso , K athleen Schmit ,
Nicolas Dejeans , H élèna Fazli , S aïd Taouji , J ohn B. Patterson ,
and E ric Chevet
14 S tudying Nitrosative Stress in Parkinson’s Disease. . . . . . . . . . . . . . . . . . . . . . 1 95
Kenny K. K. Chung
PART III PERSPECTIVES
15 C ross Talk Between ER Stress, Oxidative Stress, and Inflammation
in Health and Disease. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 205
Aditya Dandekar , R oberto Mendez , and Kezhong Zhang
16 S tress Responses During Ageing: Molecular Pathways Regulating
Protein Homeostasis. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 215
Emmanouil Kyriakakis , A ndrea Princz , and Nektarios Tavernarakis
17 T argeting Stress Responses for Regenerative Medicine. . . . . . . . . . . . . . . . . . . 2 35
Irina Milisav , S amo Ribarič , and Dušan Šuput
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 45
Contributors
YOSHINARI ANDO • Department of Biochemistry and Molecular Biology, Bloomberg School
of Public Health, J ohns Hopkins University , B altimore, M D , U SA
MEGAN ANSARI • Department of Chemistry and Biochemistry , T exas Tech University ,
Lubbock, T X, U SA
KIM B ARROSO • Inserm, U1053 , Bordeaux , France ; Université de Bordeaux , Bordeaux , France;
ER440, Oncogenesis, Stress & Signaling, Université Rennes 1, Centre de Lutte Contre le
Cancer Eugène Marquis, Rennes, France
JOHANNES BUCHNER • Munich Center for Integrated Protein Science (CIPSM)
and Department Chemie, T echnische Universität München , G arching, G ermany
SANDEEP BURMA • Division of Molecular Radiation Biology, Department of Radiation
Oncology , U niversity of Texas Southwestern Medical Center , D allas , T X, U SA
ERIC CHEVET • Inserm, U1053 , B ordeaux, F rance ; U niversité de Bordeaux , B ordeaux, F rance;
ER440, Oncogenesis, Stress & Signaling, Université Rennes 1, Centre de Lutte Contre le
Cancer Eugène Marquis, Rennes, France
KENNY K. K. CHUNG • Division of Life Science, State Key Laboratory of Molecular
Neuroscience , T he Hong Kong University of Science and Technology , H ong Kong, C hina
EMMA M. CORR • Molecular Immunology Group, School of Biochemistry and Immunology,
Trinity Biomedical Sciences Institute, T rinity College Dublin , C ollege Green,
Dublin 2, Ireland
DONAL J. COX • Molecular Immunology Group, School of Biochemistry and Immunology,
Trinity Biomedical Sciences Institute, T rinity College Dublin , C ollege Green,
Dublin 2, Ireland
CLARE C . CUNNINGHAM • Molecular Immunology Group, School of Biochemistry and
Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin , College Green,
Dublin 2, Ireland
ADITYA DANDEKAR • Department of Immunology and Microbiology, Karmanos Cancer
Institute, W ayne State University School of Medicine , D etroit, M I , U SA
NICOLAS DEJEANS • Inserm, U1053 , Bordeaux, France ; Université de Bordeaux , Bordeaux, France
VINCENT DION • Center for Integrative Genomics, U niversity of Lausanne , L ausanne,
Switzerland ; F riedrich Miescher Institute for Biomedical Research , B asel, S witzerland
MEICONG DONG • Department of Chemistry and Biochemistry , T exas Tech University ,
Lubbock, T X, U SA
LAUREN E. DRAKE • The Ben May Department for Cancer Research, The Gordon Center
for Integrative Sciences, T he University of Chicago , C hicago, I L, U SA ; T he Committee
on Molecular Pathogenesis and Molecular Medicine, The Gordon Center for Integrative
Sciences, T he University of Chicago , C hicago, I L, U SA
AISLING DUNNE • Molecular Immunology Group, School of Biochemistry and Immunology,
Trinity Biomedical Sciences Institute, T rinity College Dublin , C ollege Green,
Dublin 2, Ireland
HÉLÈNA F AZLI • Inserm, U1053 , Bordeaux , France ; Université de Bordeaux , Bordeaux , France
MITSUAKI FUJIMOTO • Departments of Biochemistry and Molecular Biology, Y amaguchi
University School of Medicine , M inami-Kogushi Ube, J apan
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