Sample Preparation Techniques for Soil, Plant, and Animal Samples PDF
Preview Sample Preparation Techniques for Soil, Plant, and Animal Samples
Handbooks Miodrag Mićić Editor Sample Preparation Techniques for Soil, Plant, and Animal Samples Springer Protocols Handbooks More information about this series at h ttp://www.springer.com/series/8623 ć ć Miodrag Mi i Editor Sample Preparation Techniques for Soil, Plant, and Animal Samples Editor Miodrag Mićić Department of Engineering Design Technology Cerritos College Norwalk , CA , USA Department of New Products Development Cerritos College Norwalk , CA , USA ISSN 1949-2448 ISSN 1949-2456 (electronic) Springer Protocols Handbooks ISBN 978-1-4939-3184-2 ISBN 978-1-4939-3185-9 (eBook) DOI 10.1007/978-1-4939-3185-9 Library of Congress Control Number: 2015955841 Springer New York Heidelberg Dordrecht London © Springer Science+Business Media New York 2016 T his work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifi cally the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfi lms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed. T he use of general descriptive names, registered names, trademarks, service marks, etc. in this publication does not imply, even in the absence of a specifi c statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. T he publisher, the authors and the editors are safe to assume that the advice and information in this book are believed to be true and accurate at the date of publication. Neither the publisher nor the authors or the editors give a warranty, express or implied, with respect to the material contained herein or for any errors or omissions that may have been made. Printed on acid-free paper Humana Press is a brand of Springer S pringer Science+Business Media LLC New York is part of Springer Science+Business Media ( w ww.springer.com ) This book is dedicated to the loving memory of my late mother, Ms. Nadežda Mićić for her unlimited love, care and support, and to the memory of my late mentors: Professor Vilim J. Vajgand, who was my fi rst chemistry professor and who, when I was a ten-year- old kid, allowed me to attend his university lectures at the Faculty of Natural Sciences and Mathematics of the University of Belgrade; Professor Predrag Polić, who was the co-advisor for my doctoral dissertation at the University of Belgrade; and Mr. Fred Andrea, former COO of ICN Biomedicals Inc. and MP Biomedicals LLC, who introduced me to the business side of product development for the biotech and life science industries. Foreword I n a Foreword the role of a writer is to introduce content and subject matter of the book and author to the public. In the case of my young colleague, Prof. Miodrag “Mickey” Mićić, Sc.D., Ph.D., M.T.M., CSWP, and his sample preparation book, it is a new book, so it is a pleasure and honor for me to do both. I have had a long and close working relationship with Dr. Mićić since he was a Vice President of Research and Development at MP Biomedicals LLC in Santa Ana, California, where he suc- cessfully developed a line of sample preparation systems used for wide arrays of applications in various fi elds of life science, the most successful and popular of which being the FastPrep® - 24 system, which becomes the workhorse of the labs dealing with diffi cult-to-lyse materials ranging from tissues samples from neural science research to the environmental samples. Prof. Mićić is, to say the least, an interesting and personable individual. The fi rst time I heard of him was actually sometime back in 1984 or 1985, when Dr. Mićić was a young kid, maybe about 10 years old, as he showed up one day to the University of Belgrade (at that time Faculty of Natural Sciences and Mathematics) to see my colleague Prof. Vilim Vajgand, and he asked to attend some lectures. He kind of become the youngest “student” there, and at that time he was featured by several major news publications in what was then the Socialist Federal Republic of Yugoslavia. I believe I fi rst met him in person around the same time, when he arrived one day to attend a lecture from some of our foreign guests at the Serbian Academy of Sciences. His passion for science and engineering continue up to this day. Fast forwarding some 20 or so years, I met Prof. Mićić again when he was hired to be a Vice President of Research and Development at MP Biomedicals (Formerly part of ICN Corporation), back in 2004, where I was the Chairman of the Scientifi c Advisory Board of the Company. Dr. Mićić interests have spread across various disciplines bridging natural sciences and engineering; this is what puts him in a unique position to be a great instrumentation developer. I have rarely encountered a person with such a diversity of knowledge and skills, both for natural sciences dis- covery and for engineering product development. He has persuaded the MP Biomedicals management to pursue a different direction, transforming it from a pure reagents house to an integrated systems manufacturer, and today the FastPrep vii viii Foreword system and other systems Dr. Mićić developed there are the fl agships of MP Biomedicals. As a book usually is a refl ection of the persona of the author or editor, his book, accordingly, is very diverse, lucid, interesting, very succinct, and to the point. To the best of my knowledge, until this book, there was no single all-inclusive resource to learn of theoretical and practical aspects of sample preparations for molecular biology, proteomics, and glycomics-related studies, especially for diffi - cult samples. As this is such a diverse and multidisciplinary fi eld involving anyone touching the life sciences area in any form, it is in my honest belief that there is no other single author who can cover it in its entirety. As such, Prof. Mićić has brought together a very unique crowd of authors. Those authors are handpicked from the combination of the best specialists in the fi eld and young rising stars, to wr ite this piece . This book for the fi rst time systematizes most of the tribal knowledge of the fi eld and sheds a further light on this process fl ow which is, for many researchers, the most occasional reason for a bottleneck in a lab. The book is virtually a must for anyone who comes into grasp with the molecular biology of any type of organism, as virtually whatever you try to study, you start by extracting its nucleic acids—and most often end up with a technical problem of how to resolve some mundane diffi culties in processing the particular sample, fi nding it that it may be both frustrating and time-consuming, and a work-stop situation. This can happen to anyone in the lab, regardless of the fi eld of work or level of experi- ence. I strongly believe that this book, with a variety of methods, protocols, and background information, can signifi cantly aid anyone in breaking such bottleneck and save time, money, and frustration. I—myself being the M.D.-Ph.D., a physician-turned-neural-scientist, who mainly practices translational research—fi nd this subject enlightening and helpful for my activities. Thereby, besides the traditional crowd of life scientists for whom this book is intended, the book will be highly benefi cial to physicians practicing the art of translational medicines as well as to any practicing pathologist, forensics/ legal medicine, molecular pathologists, and clinical diagnostics expert. To complete my short foreword statement, Prof. Mićić and the authors of this book have succeeded in organizing, summarizing, and presenting the scattered world of sample preparation information with direct practical recipes that everyone can understand and fi nd useful. While it is directed to us, who practice the art and science of molecular biology in our research or everyday practice, the book will also be of great value to trainees in all other fi elds, where high purity and integrity of biological macromolecules, be they what they may, need to be isolated from a sam- ple applying the same principles described in this book. Based on all of the above, I am excited to add this book to my bookshelf, confi dent that it will not stay long on the bookshelf, as I am sure that we will be using it regularly to shed further light on some of the problems that my colleagues and I are experiencing in our everyday practice of our neural sciences and translational medicine research. Academician Ljubiša Rakić, M.D., Ph.D. Vice President of the Serbian Academy of Sciences and Arts, Belgrade, Serbia Pref ace Sample Preparation Techniques for Soil, Plant and Animal Samples arrives to fi ll the unusual gap in the modern molecular biology lab practice collection of books. The editor of this book was surprised that, while the sample preparation for a variety of molecular biology analyses, especially from the diffi cult-to-process matrices, represents a major bottleneck in a modern molecular biology lab practices, there is no single comprehensive resource currently on the market covering its theory and practice. It is estimated that about 20% of the time spent by researchers in the molecular biology lab is actually spent on nonproductive tasks of nucleic acid sam- ple preparation, so the editor felt compelled to assemble a comprehensive treatise on the theory and practice of sample preparation of diffi cult samples, to help researchers to break the lab productivity bottleneck. For readers’ clarifi cation, I qualify as diffi cult any samples of complex mechanical matrices, which are diffi cult to grind, homogenize, and lyse, or which are “dirty,” i.e., contain other components or contaminants which may interfere with further nucleic acids purifi cation or processing. This book will cover both the theoretical foundations and practical recipes for successful sample preparation processes and tasks dealing with diffi cult samples, such as samples of plant and animal origin, and complex matrices such as food and feed, environmental samples, soils, water, and fecal matter. As such, this book appeals to a broad spectrum of practitioners doing research, diagnostics, or quality control work in broad areas, such as agro-biotech, food technology, plant science, plant breeding, environmental science, marine biology, soil microbiology, nutri- tional science, and animal breeding, up to and including law and customs enforce- ment agencies, forensics, industrial and agricultural hygiene, and many others. The book is equally appealing to anyone working at the bench, including students, graduate students, postdocs, industrial researchers, lab technicians, fi eld scientists, diagnos- tics technicians, and other similar professionals or aspiring future professionals in the life science arena, as well as the professionals working for the life science com- panies who are developing, promoting, and doing customer service supports for the instruments, tools, and kits for DNA and RNA extraction. ix
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