Open Access Medical Books



Edited by Joshua L. Heazlewood and Christopher J. Petzold .

276 pages .
Open  Access .
ISBN 978-953-307-613-3 .

In the past decade the field of proteomics has expanded from a highly technical endeavor requiring dedicated practitioners to being widely utilized by researchers of diverse backgrounds for solving complex problems in biology. The approach is used broadly to complement basic molecular and biochemical research and encompasses basic protein identification, functional characterization, comparative approaches and large-scale analyses. During this period, technical improvements (e.g., increased sensitivity, speed, mass accuracy, dynamic range) in mass spectrometric instrumentation provided a solid foundation for proteomic applications outlined in this collection.
This book is divided into four sections and is an interesting overview of the diversity and breadth of proteomic applications in biology. This is highlighted by the wide range of plant, animal and microbial species that are presented throughout the contents of this volume. Especially interesting are the variety of proteomic methods and analytical strategies employed by biological researchers. The technical side of proteomics has witnessed enormous changes in sample analysis strategies with many advanced users adopting ‘shotgun’ approaches for protein identification and quantification. In contrast, many of the studies outlined in this book employ established, but still powerful, two-dimensional gel electrophoresis strategies to array samples prior to protein identification and/or quantification. The advantages of such a visual media for assessment prior to identification are that they are useful and productive when access to high-end mass spectrometers is limited.
The first section of this book outlines the utilization of proteomics to address issues in agriculture. The increased pressure on food production in the coming decades due to expanding populations and the effects of climate change will require major reassessments of how food is produced. It is extremely likely that proteomic approaches in combination with other analysis techniques will play an important role in the adaptation of this industry through agricultural research. The chapters outlined in this section cover the utilization and application of proteomics to assess the effects of unintended post-translational modifications on food-derived proteins, an overview of approaches and techniques to examine proteins from fruit, and the use of proteomic techniques to understand viral pathogenesis in cattle.
The second section focuses on the emerging role of metaproteomics to characterize and profile microbes and microbial communities. The majority of the Earth’s biomass is comprised of microorganisms, many of which play essential roles in recycling elements such as carbon and nitrogen. While our knowledge of these complex communities is still very limited, recent advances in sequencing technologies, and now proteomics, enable detailed examination of these interesting populations. This section provides an overview of current proteomic approaches and methods being used to study microbial communities, demonstrating the utilization of these approaches to characterize a cold tolerant bacterial strain from the Antarctic.
The third section addresses the utilization of proteomics to study fundamental processes in plants. The development of novel approaches and processes using proteomics can be a direct driver for applications in other areas of biology and applied research. This section highlights the specific issues associated with undertaking proteomic analyses in plant biology, demonstrates and assesses its use in understanding the complex process of plant cell wall biosynthesis through a targeted characterization of xylan biosynthesis using multiple approaches by mass spectrometry and finally provides an overview of the subcellular isolation and proteomic characterization of the Golgi apparatus from plants and other species.
The final section highlights the use of comparative proteomics in biology to understand complex systems. One of the most significant contributions to the field of proteomics has been the development of reliable and reproducible quantitation techniques enabling comparative profiling of samples to be undertaken. This section examines the use of proteomics to identify protein markers to differentiate commercial tuna species, to identify proteins involved in pH adaptation in yeast strains, the characterization and identification of proteins in snake venom and lastly, the identification and characterization of a protein from onion involved in floral bolting.
Collectively these chapters outline studies and overviews that employ a wide variety of proteomic applications in biology. These approaches display extensive technical diversity and contrast the use of proteomics from the community level to the individual protein and together highlight the varied ways in which proteomics is being used to expand our understanding of biological systems.

Dr. Joshua L. Heazlewood
and Dr. Christopher J. Petzold
Joint BioEnergy Institute and Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley California,


Part 1 Addressing Issues in Agriculture .

 1 Food Proteomics: Mapping Modifications 3 Stefan Clerens, Jeffrey E. Plowman and Jolon M. Dyer

 2 Fruit Proteomics 33 Ariel Orellana and Ricardo Nilo

 3 Understanding the Pathogenesis of Cytopathic and Noncytopathic Bovine Viral Diarrhea Virus Infection Using Proteomics 53 Mais Ammari, Fiona McCarthy, Bindu Nanduri, George Pinchuk and Lesya Pinchuk

Part 2 Studying Environmental Complexities .

 4 Proteomics as a Tool for the Characterization of Microbial Isolates and Complex Communities 69 Florence Arsène-Ploetze, Christine Carapito, Frédéric Plewniak and Philippe N. Bertin

 5 Life in the Cold: Proteomics of the Antarctic Bacterium Pseudoalteromonas haloplanktis 93 Florence Piette, Caroline Struvay, Amandine Godin, Alexandre Cipolla and Georges Feller

Part 3 Diverse Impacts in Plant Proteomics .

 6 Plant Protein Analysis 117 Alessio Malcevschi and Nelson Marmiroli

 7 Assessment of Proteomics Strategies for Plant Cell Wall Glycosyltransferases in Wheat, a Non-Model Species: Glucurono(Arabino)Xylan as a Case Study 143 Faik Ahmed

 8 The Current State of the Golgi Proteomes 167 Harriet T. Parsons, Jun Ito, Eunsook Park, Andrew W. Carroll, Hiren J. Joshi, Christopher J. Petzold, Georgia Drakakaki and Joshua L. Heazlewood

Part 4 Comparative Approaches in Biology .

 9 Differentiation of Four Tuna Species by Two-Dimensional Electrophoresis and Mass Spectrometric Analysis 191 Tiziana Pepe, Marina Ceruso, Andrea Carpentieri, Iole Ventrone, Angela Amoresano, Aniello Anastasio and Maria Luisa Cortesi

10 Identification of Proteins Involved in pH Adaptation in Extremophile Yeast Yarrowia lipolytica 209 Ekaterina Epova, Marina Guseva, Leonid Kovalyov, Elena Isakova, Yulia Deryabina, Alla Belyakova, Marina Zylkova and Alexei Shevelev

 11 The Role of Conventional Two-Dimensional Electrophoresis (2DE) and Its Newer Applications in the Study of Snake Venoms 225 Jaya Vejayan, Mei San Tang and Ibrahim Halijah

 12 Protein Homologous to Human CHD1, Which Interacts with Active Chromatin (HMTase) from Onion Plants 253 DongYun Hyun and Hong-Yul Seo .

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Published by: younes younes - Thursday, June 27, 2013


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