Me t h o d s in M Bi o l o g y - newbooks-services.de€¦ · Lipidomics Volume 2: Methods and Protocols Edited by Donald Armstrong University at Buffalo, Buffalo, NY, USA University

BookID 188547_ChapID FM_Proof# 1 - 09/07/2009

M e t h o d s i n M o l e c u l a r B i o l o g y ™

Series EditorJohn M. Walker

School of Life SciencesUniversity of Hertfordshire

Hatfield, Hertfordshire, AL10 9AB, UK

For other titles published in this series, go to www.springer.com/series/7651


Lipidomics

Volume 2: Methods and Protocols

Edited by

Donald Armstrong

University at Buffalo, Buffalo, NY, USA University of Florida, Gainesville, FL, USA


EditorDonald ArmstrongUniversity of BuffaloBuffalo, NY, USAandUniversity of FloridaGainesville, FL, USA

The cover image are overlapping snapshots of a single peroxidized lipid, taken from computer stimu-lations. Peroxidation mofidies the local conformational preferences of acyl chains and increases their mobility, with implications for structural and dynamic properties of the membrane.

ISSN 1064-3745 e-ISSN 1940-6029ISBN 978-1-60761-324-4 e-ISBN 978-1-60761-325-1DOI 10.1007/978-1-60761-325-1Springer New York Dordrecht Heidelberg London

Library of Congress Control Number: 2009927725

© Humana Press, a part of Springer Science+Business Media, LLC 2009All rights reserved. This work may not be translated or copied in whole or in part without the written permission of the publisher (Humana Press, c/o Springer Science+Business Media, LLC, 233 Spring Street, New York, NY 10013, USA), except for brief excerpts in connection with reviews or scholarly analysis. Use in connection with any form of information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed is forbidden.The use in this publication of trade names, trademarks, service marks, and similar terms, even if they are not identified as such, is not to be taken as an expression of opinion as to whether or not they are subject to proprietary rights.While the advice and information in this book are believed to be true and accurate at the date of going to press, neither the authors nor the editors nor the publisher can accept any legal responsibility for any errors or omissions that may be made. The publisher makes no warranty, express or implied, with respect to the material contained herein.

Cover illustration: Snapshots of a single PLPC and a peroxidized analogue (13-tc), taken at 5 ns intervals. Molecules are oriented along the membrane and superimposition was done on the phosphorus and oxygen atoms. Images were obtained from Chapter 18, Vol. 1.

Cover design: Karen Schulz

Printed on acid-free paper

Humana Press is part of Springer Science+Business Media (www.springer.com)


Preface

Lipidomics is a sub-discipline of metabolomics and is defined as the large-scale study of non-water-soluble metabolites (lipids and lipidome) that utilize system-level analysis to characterize lipids and their interacting moieties (1). A literature search at the end of 2008 showed there were 200 articles published on lipidomics encompassing glycerophospholi-pids, sphingolipids, polyunsaturated fatty acids, glycolipids, sterol lipids, and proteolipids. It has been predicted that the combination of these lipid classes totals between 1,000 and 2,000 molecules. Lipids can also act as s econd messengers, or mitogens, and participate in profiling and signaling via specialized microdomains that have large amounts of lipids. When lipids are disturbed, their metabolites probably contribute to disease. In prostate cancer, for example, cyclooxygenase and lipooxygenase are upregulated reducing angio-genesis and tumor growth.

Early separation and identification of lipids started with TLC, and as technol-ogy advanced, it progressed to the use of GC and HPLC. Technical improvements to HPLC include reversed-phase methods, ESI, evaporative light scattering, electrochemical detection, APCI, suppressed conductivity and multi-dimensional electrophoresis. Other technologies coupled to chromatographic methods, such as MS/MS-MSn/MALDI/TOF, NMR, and MRM, provide a powerful approach to the global analysis of complex lipid mixtures, understanding structural changes through biophysical approaches and the effects of lipids on physiology, i.e. atherosclerosis. This has given us a clearer under-standing of human and animal pathology, i.e. diabetes, cancer, neurodegeneration, and infectious disease. A new approach to measure oxidized lipids, referred to as “oxidative lipidomics,” has recently been described which provides methodology for separation and identification of these highly reactive lipids, especially in mitochondria. Many novel tech-niques are described in these volumes, including an imaging lipidomics approach. For another lipidomic approach of a lipid-derived radical technique, the reader is referred to Iwabashi, H., 2008. Advanced Protocols in Oxidative Stress I, volume 477, Chapter 6, Humana Press. In that same volume, a lipidomics technique for sphingolipids is also described, i.e. Wilder, AJ and Cowart, LA, Chapter 28.

The present volumes have taken a “shotgun” approach and are divided into seven parts in order to include as many different varieties of technology as possible. Chapters by international experts present a wide variety of reviewed as well as unpublished data on isolation techniques, structural analysis, lipid rafts, lipid trafficking and profiling, biomark-ers, lipid peroxidation, biostatistics applied to lipids, software tools, and bioinformatics. These studies range from simple systems, such as in yeast, to complex biological models.

The ever increasing utilization of lipidomics will lead to more powerful technology, improved diagnostic–prognostic capabilities for medical disorders, and for the identifica-tion of new classes of lipids.

v


vi Preface

I thank my son, Dennis Armstrong, and my grandson, David Armstrong of On-Staff Technology, Inc., for assistance with technical support, information technology, and multi-media services.

Buffalo, NY Donald ArmstrongGainesville, FL

Reference

1. Wenk, M.R. 2005. The emerging field of lipidomics. Nature Reviews 4: 595–610.


Contents

Preface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vContributors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix

Part I OxIdIzed LIPIds

1 F2-Isoprostanes: Sensitive Biomarkers of Oxidative Stress In Vitro and In Vivo: A Gas Chromatography-Mass Spectrometric Approach . . . . . . . . . . . 3Ingrid Wiswedel

2 Volatile Oxylipins and Related Compounds Formed Under Stress in Plants. . . . . . 17Kenji Matsui, Koichi Sugimoto, Pattana Kakumyan, Sergey A. Khorobrykh, and Jun’ichi Mano

3 Quantification of Lysophosphatidylcholine Species by High-Throughput Electrospray Ionization Tandem Mass Spectrometry (ESI-MS/MS) . . . . . . . . . . . 29Gerhard Liebisch and Gerd Schmitz

4 Use of Lipidomics for Analyzing Glycerolipid and Cholesteryl Ester Oxidation by Gas Chromatography, HPLC, and On-line MS . . . . . . . . . . . . . . . . 39Arnis Kuksis, Jukka-Pekka Suomela, Marko Tarvainen, and Heikki Kallio

5 Lipid Raft Redox Signaling Platforms in Plasma Membrane . . . . . . . . . . . . . . . . . 93Fan Yi, Si Jin, and Pin-Lan Li

6 Mass Spectrometry Analysis of Polyisoprenoids Alcohols and Carotenoids via ESI(Li +)-MS/MS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 109Fabio Luiz D’Alexandri, Renata Tonhosolo, Emilia A. Kimura, and Alejandro Miguel Katzin

7 Detection of a Lipid-Lysine Adduct Family with an Amide-Bond as the Linkage: Novel Markers for Lipid-Derived Protein Modifications . . . . . . . . 129Yoji Kato and Toshihiko Osawa

8 Assessing the Neuroprotective Effect of Antioxidative Food Factors by Application of Lipid-Derived Dopamine Modification Adducts. . . . . . . . . . . . . 143Xuebo Liu, Naruomi Yamada, and Toshihiko Osawa

9 Mass-Spectrometric Characterization of Phospholipids and Their Hydroperoxide-Derivatives In Vivo: Effects of Total Body Irradiation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153Yulia Y. Tyurina, Vladimir A. Tyurin, Valentina I. Kapralova, Andrew A. Amoscato, Michael W. Epperly, Joel S. Greenberger, and Valerian E. Kagan

Part II traffIckIng and PrOfILIng

10 Comprehensive mRNA Profiling of Lipid-Related Genes in Microglia and Macrophages Using Taqman Arrays . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 187Richard Mauerer, Yana Walczak, and Thomas Langmann

vii


viii Contents

11 Imaging Lipid Membrane Domains with Lipid-Specific Probes. . . . . . . . . . . . . . . 203Françoise Hullin-Matsuda, Reiko Ishitsuka, Miwa Takahashi, and Toshihide Kobayashi

12 Monitoring Sterol Uptake, Acetylation, and Export in Yeast . . . . . . . . . . . . . . . . . 221Vineet Choudhary and Roger Schneiter

13 Methods to Monitor Fatty Acid Transport Proceeding Through Vectorial Acylation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 233Elsa Arias-Barrau, Concetta C. DiRusso, and Paul N. Black

14 Activity-Based Profiling of Lipases in Living Cells . . . . . . . . . . . . . . . . . . . . . . . . . 251Maximilian Schicher, Iris Jesse, and Ruth Birner-Gruenberger

15 Histochemistry and Lipid Profiling Combine for Insights into Aging and Age-Related Maculopathy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 267Christine A. Curcio, Martin Rudolf, and Lan Wang

Part III sOftware and BIOInfOrmatIcs

16 Instrument-Independent Software Tools for the Analysis of MS–MS and LC–MS Lipidomics Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 285Perttu Haimi, Krishna Chaithanya, Ville Kainu, Martin Hermansson, and Pentti Somerharju

17 Computer-Assisted Interpretation of Triacylglycerols Mass Spectra . . . . . . . . . . . . 295Josef Cvacka and Edita Kofroňová

18 Visualization of Complex Processes in Lipid Systems Using Computer Simulations and Molecular Graphics. . . . . . . . . . . . . . . . . . . . . . . . . . . 317Jelena Telenius, Ilpo Vattulainen, and Luca Monticelli

19 Bioinformatics Strategies for the Analysis of Lipids . . . . . . . . . . . . . . . . . . . . . . . . 339Craig E. Wheelock, Susumu Goto, Laxman Yetukuri, Fabio Luiz D’Alexandri, Christian Klukas, Falk Schreiber, and Matej Orešicč

Part IV BIOstatIstIcs

20 The Effect of Lipid Adjustment on the Analysis of Environmental Contaminants and the Outcome of Human Health Risks . . . . . . . . . . . . . . . . . . . 371Audrey J. Gaskins and Enrique F. Schisterman

Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 383


Contributors

andrew a. amOscatO • Department of Pathology, University of Pittsburgh, Pittsburgh, PA, USA

eLsa arIas-Barrau • Department of Biochemistry, University of Nebraska, Lincoln, NE, USA

ruth BIrner-gruenBerger • ZMF Center for Medical Research, Medical University of Graz, Graz, Austria

PauL n. BLack • Department of Biochemistry, University of Nebraska, Lincoln, NE, USA

krIshna B. chaIthanya • Department of Biochemistry, Institute of Biomedicine, University of Helsinki, Helsinki, Finland

VIneet chOudhary • Department of Medicine, Division of Biochemistry, University of Fribourg, Fribourg, Switzerland

chrIstIne a. curcIO • Department of Ophthalmology, Callahan Eye Foundation Hospital, University of Alabama School of Medicine, Birmingham, AL, USA

JOsef cVačka • Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic

faBIO LuIz d’aLexandrI • Department of Medical Biochemistry and Biophysics, Division of Physiological Chemistry II, Karolinska Institutet, Stockholm, Sweden Department of Parasitology, Department of Biochemical Sciences, University of San Paulo, San Paulo, Brazil

cOncetta c. dIrussO • Department of Biochemistry and Nutrition and Health Sciences, University of Nebraska, Lincoln, NE, USA

mIchaeL w. ePPerLy • Department of Radiation Oncology, University of Pittsburgh, Pittsburgh, PA, USA

audrey J. gaskIns • Division of Epidemiology, Statistics and Prevention Research, Eunice Kennedy Schriver National Institute of Child Health and Human Development, NIH, Rockville, MD, USA

susumu gOtO • Bioinformatics Center, Institute for Chemical Research, Kyoto University, Kyoto, Japan

JOeL s. greenBerger • Department of Radiation Oncology, University of Pittsburgh, Pittsburgh, PA, USA

Perttu haImI • Department of Biochemistry, Institute of Biomedicine, University of Helsinki, Helsinki, Finland

martIn hermanssOn • Department of Biochemistry, Institute of Biomedicine, University of Helsinki, Helsinki, Finland

francOIse huLLIn-matsuda • INSERM-RIKEN Lipidomics Unit, Lipid Biology Laboratory, RIKEN Advanced Science Institute, Saitama, Japan

reIkO IshItsuka • VCAD System Research Program, Bio-Research Infrastructure Construction Team, RIKEN, Saitama, Japan

IrIs Jesse • Institute of Biochemistry, Graz University, Graz, Austria

ix

BookID 188547_ChapID FM_Proof# 1 - 09/07/2009 BookID 188547_ChapID FM_Proof# 1 - 09/07/2009

x Contributors

sI JIn • Department of Pharmacology & Toxicology, Medical College of Virginia Campus, Virginia Commonwealth University, Richmond, VA, USA

VaLerIan e. kagan • Center for Free Radical and Antioxidant Health and Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA, USA

VILLe kaInu • Department of Biochemistry, Institute of Biomedicine, University of Helsinki, Helsinki, Finland

Pattana kakumyan • Department of Biological Chemistry, Faculty of Agriculture and Department of Applied Molecular Bioscience, Graduate School of Medicine, Yamaguchi University, Yamaguchi, Japan

heIkkI kaLLIO • Department of Biochemistry and Food Chemistry, University of Turku, Turku, Finland

VaLentIna I. kaPrasLOVa • Center for Free Radical and Antioxidant Health, and Department of Environmental & Occupational Health, University of Pittsburgh, Pittsburgh, PA, USA

yOJI katO • Laboratory of Food and Biodynamics, Nagoya University Graduate School of Bioagricultural Sciences, Chikusa, Japan

aLeJandrO mIgueL katzIn • Department of Parasitology, Institute of Sciences, University of San Paulo, San Paulo, Brazil

sergey a. khOrOBrykh • Science Research Center, Yamaguchi University, Yamaguchi, Japan; Institute of Basic Biological Problems, Russian Academy of Sciences, Moscow, Russia

emILIa a. kImura • Department of Parasitology, Institute of Biomedical Sciences, University of San Paulo, San Paulo, Brazil

chrIstIan kLukas • Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany

tOshIhIde kOBayashI • Lipid Biology Laboratory/INSERN-RIKEN Lipidomics Unit, RIKEN, Saitama, Japan; INSERM U870/INRA U1235/INSA, University of Lyon, Lyon, France

edIta kOfrOňOVà • Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic

arnIs kuksIs • Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, Canada

thOmas Langmann • Institute of Human Genetics, University of Regensburg, Regensburg, Germany

PIn-Lan LI • Department of Pharmacology and Toxicology, Medical College of Virginia Campus, Virginia Commonwealth University, Richmond, VA, USA

gerhard LIeBIsch • Institute of Clinical Chemistry and Laboratory Medicine, University of Regensburg, Regensburg, Germany

xueBO LIu • Laboratory of Food and Biodynamics, Nagoya University Graduate School of Bioagricultural Sciences, Chikusa, Japan

Jun’IchI manO • Institute of Basic Biological Problems, Russian Academy of Science, Moscow, Russia


Contributors xi

kenJI matsuI • Department of Biological Chemistry, Faculty of Agriculture and Department of Applied Molecular Bioscience, Graduate School of Medicine, Yamaguchi University, Yamaguchi, Japan

rIchard mauerer • Synlab Medical Care Service, Medical Care Center, Weiden, Germany

Luca mOntIceLLI • Department of Applied Physics, Helsinki University of Technology, Espoo, Finland; Department of Physics, Tampere University of Technology, Tampere, Finland

mateJ OrešIč • VTT Technical Research Centre of Finland, Espoo, FinlandtOshIhIkO Osawa • Laboratory of Food and Biodynamics, Nagoya University

Graduate School of Bioagricultural Sciences, Chikusa, JapanmartIn rudOLf • University Eye Hospital, Lubeck, Universitatsklinikum,

Schleswig-Holstein, Lubeck, GermanymaxImILIan schIcher • Institute of Biochemistry, University of Graz, Graz, AustriaenrIque schIsterman • Division of Epidemiology, Statistics and Preventive Research,

Eunice Kennedy Schriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA

gerd schmItz • Institute for Clinical Chemistry and Laboratory Medicine, University Hospital, Regensburg, Regensburg, Germany

rOger schneIter • Department of Medicine, Division of Biochemistry, University of Fribourg, Fribourg, Switzerland

faLk schreIBer • Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben and Institute of Computer Science, Martin-Luther-University, Halle-Wittenberg, Germany

PenttI sOmerharJu • Department of Biochemistry, Institute of Biomedicine, University of Helsinki, Helsinki, Finland

kOIchI sugImOtO • Department of Biological Chemistry, Faculty of Agriculture and Applied Molecular Bioscience, Graduate School of Medicine, Yamaguchi University, Yamaguchi, Japan; Center for Ecological Research, Kyoto University, Kyoto, Japan

Jukka-Pekka suOmeLa • Department of Biochemistry and Food Chemistry, University of Turku, Turku, Finland

mIwa takahashI • VCAD System Research Program, BioResearch Infrastructure Construction Team, RIKEN, Saitama, Japan

markO tarVaInen • Department of Biochemistry and Food Chemistry, University of Turku, Turku, Finland

JeLena teLenIus • Department of Applied Physics, Helsinki University of Technology, Espoo, Finland

renata tOnhOsOLO • Department of Parasitology, Institute of Biomedical Sciences, University of San Paulo, San Paulo, Brazil

VLadImIr a. tyurIn • Center for Free Radical and Antioxidant Health and Department of Environmental & Occupational Health, University of Pittsburgh, Pittsburgh, PA, USA

yuLIa y. tyurIna • Center for Free Radical and Antioxidant Health and Department of Environmental & Occupational Health, University of Pittsburgh, Pittsburgh, PA, USA


xii Contributors

ILPO VattuLaInen • Department of Applied Physics, Helsinki University of Technology, Espoo, Finland; Department of Physics, Tampere University of Technology, Tampere, Finland MEMPHYS – Center for Biomembrane Physics, Physics Department, University of Southern Denmark, Odense, Denmark

yana waLczak • Institute of Human Genetics, University of Regensburg, Regensburg, Germany

Lan wang • Department of Ophthalmology, Callahan Eye Foundation Hospital, University of Alabama School of Medicine, Birmingham, AL, USA

craIg e. wheeLOck • Department of Medical Biochemistry and Biophysics, Division of Physical Chemistry II, Karolinska Institutet, Stockholm, Sweden Bioinformatics Center, Institute for Chemical Research, Kyoto University, Kyoto, Japan

IngrId wIswedeL • Department of Pathological Biochemistry, Medical Faculty of the Otto-von-Guericke-University, Magdeburg, Germany

naruOmI yamada • Laboratory of Food and Biodynamics, Nagoya University Graduate School of Bioagricultural Sciences, Chikusa, Japan

Laxman yetukurI • VTT Technical Research Centre of Finland, Espoo, Finlandfan yI • Department of Pharmacology & Toxicology, Medical College of Virginia

Campus, Virginia Commonwealth University, Richmond, VA, USA

http://www.springer.com/978-1-60761-324-4

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Me t h o d s in M Bi o l o g y - newbooks-services.de€¦ · Lipidomics Volume 2: Methods and Protocols Edited by Donald Armstrong University at Buffalo, Buffalo, NY, USA University