POLYMERASE CHAIN REACTION Edited by Patricia Hernandez-Rodriguez and Arlen Patricia Ramirez Gomez Polymerase Chain Reaction Edited by Patricia Hernandez-Rodriguez and Arlen Patricia Ramirez Gomez Published by InTech Janeza Trdine 9, 51000 Rijeka, Croatia Copyright © 2012 InTech All chapters are Open Access distributed under the Creative Commons Attribution 3.0 license, which allows users to download, copy and build upon published articles even for commercial purposes, as long as the author and publisher are properly credited, which ensures maximum dissemination and a wider impact of our publications. After this work has been published by InTech, authors have the right to republish it, in whole or part, in any publication of which they are the author, and to make other personal use of the work. Any republication, referencing or personal use of the work must explicitly identify the original source. As for readers, this license allows users to download, copy and build upon published chapters even for commercial purposes, as long as the author and publisher are properly credited, which ensures maximum dissemination and a wider impact of our publications. Notice Statements and opinions expressed in the chapters are these of the individual contributors and not necessarily those of the editors or publisher. No responsibility is accepted for the accuracy of information contained in the published chapters. The publisher assumes no responsibility for any damage or injury to persons or property arising out of the use of any materials, instructions, methods or ideas contained in the book. Publishing Process Manager Bojan Rafaj Technical Editor Teodora Smiljanic Cover Designer InTech Design Team First published May, 2012 Printed in Croatia A free online edition of this book is available at www.intechopen.com Additional hard copies can be obtained from orders@intechopen.com Polymerase Chain Reaction, Edited by Patricia Hernandez-Rodriguez and Arlen Patricia Ramirez Gomez p. cm. ISBN 978-953-51-0612-8 Contents Preface IX Chapter 1 Application of PCR in Diagnosis of Peste des Petits Ruminants Virus (PPRV) 1 Muhammad Abubakar, Farida Mehmood, Aeman Jeelani and Muhammad Javed Arshed Chapter 2 Application of PCR-Based Methods to Dairy Products and to Non-Dairy Probiotic Products 11 Christophe Monnet and Bojana Bogovič Matijašić Chapter 3 Role of Polymerase Chain Reaction in Forensic Entomology 51 Tock Hing Chua and Y. V. Chong Chapter 4 PCR for Screening Potential Probiotic Lactobacilli for Piglets 65 Maurilia Rojas-Contreras, María Esther Macías-Rodríguez and José Alfredo Guevara Franco Chapter 5 Polymerase Chain Reaction for Phytoplasmas Detection 91 Duška Delić Chapter 6 Molecular Diagnostics of Mycoplasmas: Perspectives from the Microbiology Standpoint 119 Saúl Flores-Medina, Diana Mercedes Soriano-Becerril and Francisco Javier Díaz-García Chapter 7 BRAF V600E Mutation Detection Using High Resolution Probe Melting Analysis 143 Jennifer E. Hardingham, Ann Chua, Joseph W. Wrin, Aravind Shivasami, Irene Kanter, Niall C. Tebbutt and Timothy J. Price Chapter 8 Polymerase Chain Reaction: Types, Utilities and Limitations 157 Patricia Hernández-Rodríguez and Arlen Gomez Ramirez VI Contents Chapter 9 The Application of PCR-Based Methods in Food Control Agencies – A Review 173 Azuka Iwobi, Ingrid Huber and Ulrich Busch Chapter 10 PCR in Food Analysis 195 Anja Klančnik, Minka Kovač, Nataša Toplak, Saša Piskernik and Barbara Jeršek Chapter 11 PCR in Disease Diagnosis of WND 221 Asifa Majeed, Abdul Khaliq Naveed, Natasha Rehman and Suhail Razak Chapter 12 Real-Time PCR for Gene Expression Analysis 229 Akin Yilmaz, Hacer Ilke Onen, Ebru Alp and Sevda Menevse Chapter 13 Recent Advances and Applications of Transgenic Animal Technology 255 Xiangyang Miao Chapter 14 Measuring of DNA Damage by Quantitative PCR 283 Ayse Gul Mutlu Chapter 15 Detection of Apple Chlorotic Leaf Spot Virus in Tissues of Pear Using In Situ RT-PCR and Primed In Situ Labeling 295 Na Liu, Jianxin Niu and Ying Zhao Chapter 16 Application of PCR Technologies to Humans, Animals, Plants and Pathogens from Central Africa 309 Ouwe Missi Oukem-Boyer Odile, Migot-Nabias Florence, Born Céline, Aubouy Agnès and Nkenfou Céline Chapter 17 Study of Mycobacterium Tuberculosis by Molecular Methods in Northeast Mexico 349 H. W. Araujo-Torres, J. A. Narváez-Zapata, M. G. Castillo-Álvarez, MS. Puga-Hernández, J. Flores-Gracia and M. A. Reyes-López Chapter 18 Development of a Molecular Platform for GMO Detection in Food and Feed on the Basis of “Combinatory qPCR” Technology 363 Sylvia Broeders, Nina Papazova, Marc Van den Bulcke and Nancy Roosens Chapter 19 Overview of Real-Time PCR Principles 405 Morteza Seifi, Asghar Ghasemi, Siamak Heidarzadeh, Mahmood Khosravi, Atefeh Namipashaki, Vahid Mehri Soofiany, Ali Alizadeh Khosroshahi and Nasim Danaei Contents VII Chapter 20 PCR Advances Towards the Identification of Individual and Mixed Populations of Biotechnology Microbes 443 P. S. Shwed Chapter 21 Lack of Evidence for Contribution of eNOS, ACE and AT1R Gene Polymorphisms with Development of Ischemic Stroke in Turkish Subjects in Trakya Region 455 Tammam Sipahi Chapter 22 Analysis of Genomic Instability and Tumor-Specific Genetic Alterations by Arbitrarily Primed PCR 469 Nikola Tanic, Jasna Bankovic and Nasta Tanic Chapter 23 Analysis of Alternatively Spliced Domains in Multimodular Gene Products - The Extracellular Matrix Glycoprotein Tenascin C 487 Ursula Theocharidis and Andreas Faissner Chapter 24 Submicroscopic Human Parasitic Infections 501 Fousseyni S. Touré Ndouo Chapter 25 Identification of Genetic Markers Using Polymerase Chain Reaction (PCR) in Graves’ Hyperthyroidism 517 P. Veeramuthumari and W. Isabel Chapter 26 Detection of Bacterial Pathogens in River Water Using Multiplex-PCR 531 C. N. Wose Kinge, M. Mbewe and N. P. Sithebe Chapter 27 PCR-RFLP and Real-Time PCR Techniques in Molecular Cancer Investigations 555 Uzay Gormus, Nur Selvi and Ilhan Yaylim-Eraltan Preface This book is intended to present current concepts in molecular biology with the emphasis on the application to animal, plant and human pathology, in various aspects such as etiology, diagnosis, prognosis, treatment and prevention of diseases as well as the use of these methodologies in understanding the pathophysiology of various diseases that affect living beings. It is known today that molecular biology has revolutionized the study and understanding of health and disease. Significant developments occurred after 1953, based on the impact generated in many disciplines, especially those life-related such as medicine. Furthermore, the advances in molecular biology have revolutionized industry, agriculture, pharmacology, and animal and plant production, among others. Technology based on Molecular Chain reaction Polymerase (PCR) is advancing rapidly since it is fundamental for improving the health of all living beings. Importantly, the most of the research in biology and medicine requires a series of molecular strategies that allow the generation of new knowledge, in order to enable better understanding of the mechanisms of life and the cellular changes that affect all living things. Molecular biology has transformed the way we see and understand the physiological and pathological changes of cells, organs and systems. In this sense, this book presents the fundamentals, applications, advantages and disadvantages of various molecular techniques from the research process in biology, medicine, agriculture and environment in basic and applied science. Each chapter explains molecular techniques through various experiments offering new knowledge in different disciplines with applications trying to ultimately improve the conditions of life. The book includes the participation of different authors and co-authors of various nationalities, all of them experts in the field. The book will be useful to professionals, students, teachers and researchers interested in expanding their knowledge in molecular biology, one of the most exciting areas of work today. X Preface I am grateful for the possibility of editing this book and sending a message to all readers: perform with passion, responsibility and dedication your projects in life; in my case – it is the research. Patricia Hernandez-Rodriguez Universidad De La Salle, Bogota, Colombia [...]... Morbilliviruses consists of a single strand of RNA, it must be first copied into DNA, using reverse transcriptase, in a two-step reaction known as reverse transcription polymerase chain reaction (RT-PCR).Among the various techniques developed for the detection of PPRV, however, polymerase chain reaction (PCR) technique developed using F-gene primers has been the most popular tool so far, for diagnosis as well... the polymerase chain reaction (PCR), has proved invaluable for analysis of such poorly preserved field samples The PCR test consists of repetitive cycles of DNA denaturation, primer annealing and extension by a DNA polymerase effectively doubling the target with each cycle leading, theoretically, to an exponential rise in DNA product There placement of the polymerase now fragment by thermo-stable polymerase. .. 268 – 274 10 Polymerase Chain Reaction [31] Abubakar M, HA Khan, MJ Arshed, M Hussain M and Ali Q, 2011 Peste des petits ruminants (PPR): Disease appraisal with global and Pakistan perspective Small Rum Res, 96: 1–10 [32] Couacy-Hymann, E., Roger, F., Hurard, C., Guillou, J.P., Libeau, G., Diallo,A., 2002 Rapid andsensitive detection of peste despetitsruminants virus by a polymerase chain reaction assay... target sequences are fused to both ends of a non-target fragment, to which a second fluorescent probe (the IAC probe) hybridises The simultaneous use in a single reaction of two differently labelled fluorescent probes makes it 22 Polymerase Chain Reaction possible to quantify the target and to assess PCR efficiency at the same time If negative results are obtained for the target PCR, the absence of a positive... situations • • * Morbidity rate in susceptible populations can reach 90–100% Mortality rates vary among susceptible animals but can reach 50–100% in more severe instances Corresponding Author 2 Polymerase Chain Reaction • Both morbidity and mortality rates are lower in endemic areas and in adult animals when compared to young ones Lineage 1 Lineage 2 Lineage 3 Lineage 4 Uncharacterised Fig 1 Geographic... antigenome promoter includes the trailer sequence and the untranslated regions of the L gene at 5’ end Gene start (GS) and gene end (GE), enclosing the intergenic trinucleotide motifs are also shown 4 Polymerase Chain Reaction Fig 3 Genome of PPR virus b Antigenic and Immunogenic Epitopes: Surface glycoproteins hemagglutinin (H) and fusion protein (F) of morbilliviruses are highly immmunogenic and helps in... obtained, the assay appeared to be the test of choice for PPRV detection Relative specificity and sensitivity of F-gene based RT-PCR with sandwich-ELISA was 100 and 12.5 percent, respectively 31 8 Polymerase Chain Reaction 6 Conclusion The conventional techniques are largely replaced by genome-based detection techniques for the diagnosis and confirmation of PPR virus Molecular-biological techniques such... L., Kitching, R.P and Barrett, T (1996) Geographic distribution and epidemiology of peste des petits ruminants viruses Virus Res 43: 149-153 [8] Forsyth, M.A and T Barrett, 1995 Evaluation of polymerase chain reaction for the detection and characterization of rinderpest and peste des petits ruminants viruses for epidemiological studies Virus Res 39: 151–63 [9] Farooq, U., Q.M khan and T Barrett (2008)... Micro 22: 341-352.Taylor, W.P (1979a) Protection of goats against PPR with attenuated RP virus Res Vet Sci 27: 321-324 [24] Barrett, T., C Amarel-Doel, R.P Kitching and A Gusev, 1993a Use of the polymerase chain reaction in differentiating rinderpest field virus and vaccine virus in the same animals Rev Sci Tech Off Int Epiz., 12: 865–72 [25] Dowling, P.C., Blumberg, B.M., Menonna, J., Adamus, J.E., Cook,... in cell culture The fragility of morbillivirus virions generally renders techniques such as virus isolation redundant for routine diagnostic use, especially where sample quality is poor Such 6 Polymerase Chain Reaction techniques are also considered to be time-consuming and cumbersome Virus isolation does, however, play an important role from a research perspective ELISA tests using monoclonal antibodies . a two-step reaction known as reverse transcription polymerase chain reaction (RT-PCR).Among the various techniques developed for the detection of PPRV, however, polymerase chain reaction (PCR). POLYMERASE CHAIN REACTION Edited by Patricia Hernandez-Rodriguez and Arlen Patricia Ramirez Gomez Polymerase Chain Reaction Edited by Patricia. Probiotic Products 11 Christophe Monnet and Bojana Bogovič Matijašić Chapter 3 Role of Polymerase Chain Reaction in Forensic Entomology 51 Tock Hing Chua and Y. V. Chong Chapter 4 PCR for