POINT MUTATION Edited by Colin Logie Point Mutation Edited by Colin Logie 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 Sandra Bakic Technical Editor Teodora Smiljanic Cover Designer InTech Design Team First published March, 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.org Point Mutation, Edited by Colin Logie p. cm. ISBN 978-953-51-0331-8 Contents Preface IX Part 1 Current Views on Point Mutation Theory 1 Chapter 1 Point Mutations, Their Transition Rates and Involvements in Human and Animal Disorders 3 Viliam Šnábel Chapter 2 Bioinformatical Analysis of Point Mutations in Human Genome 15 Branko Borštnik and Danilo Pumpernik Chapter 3 Estimating Human Point Mutation Rates from Codon Substitution Rates 31 Kazuharu Misawa Part 2 Point Mutation in Viruses: From Drug Resistance to Vaccination 43 Chapter 4 Point Mutations and Antiviral Drug Resistance 45 José Arellano-Galindo, Blanca Lilia Barron, Yetlanezi Vargas-Infante, Enrique Santos-Esteban, Emma del Carmen Herrera-Martinez, Norma Velazquez-Guadarrama and Gustavo Reyes-Teran Chapter 5 Point Mutations Associated with HIV-1 Drug Resistance, Evasion of the Immune Response and AIDS Pathogenesis 93 Makobetsa Khati and Laura Millroy Chapter 6 Recombination and Point Mutations in Type G Rotavirus Strains: The Challenges of Vaccine Development 133 Abid Nabil Ben Salem, Rouis Zyed, Buesa Javier and Aouni Mahjoub VI Contents Chapter 7 Molecular Attenuation Process in Live Vaccine Generation for Arenaviruses 159 Sandra Elizabeth Goñi and Mario Enrique Lozano Part 3 Point Mutation in Bacteria: Human Activity-Driven Evolution 183 Chapter 8 Mutational Polymorphism in the Bacterial Topoisomerase Genes Driven by Treatment with Quinolones 185 Maja Velhner and Dragica Stojanović Part 4 Point Mutation in Eukaryote: From Pathogens to Cigarette Smoke 211 Chapter 9 Point Mutation in Surveillance of Drug-Resistant Malaria 213 Sungano Mharakurwa Chapter 10 Correlations with Point Mutations and Severity of Hemolitic Anemias: The Example of Hereditary Persistence of Fetal Hemoglobin with Sickle Cell Anemia and Beta Thalassemia 227 Anderson Ferreira da Cunha, Iran Malavazi, Karen Simone Romanello and Cintia do Couto Mascarenhas Chapter 11 Point Mutations That Reduce Erythrocyte Resistance to Oxidative Stress 255 Dmitriy Volosnikov and Elena Serebryakova Chapter 12 Point Mutations in Ferroportin Disease: Genotype/Phenotype Correlation 285 Riad Akoum Chapter 13 p53: Point Mutations, SNPs and Cancer 301 Ming Fang, Iva Simeonova and Franck Toledo Chapter 14 Transgenerational Effects of Maternal Nicotine Exposure During Gestation and Lactation on the Respiratory System 323 G. S. Maritz Chapter 15 Synthetic Point Mutagenesis 335 Roman A.G. Schaeken, Joke J.F.A. van Vugt and Colin Logie Preface Point mutation is a vast subject that could not be captured in a set of fifteen vignettes. This book therefore reflects the interest of its authors, who are, for the most part, medically oriented scientists from all over the world, from Latin America to Russia and from Africa to Asia. A diverse array of research fields are broached, with an effort to bring the reader up to date with the knowledge amassed since the year 2000. After an introductory chapter on point mutation, current theory is expounded in two chapters on human point mutation. This is followed by five chapters on point mutation in viral genomes, going from adaptation of HIV to current therapies to antiviral vaccination and point mutation. Next, current trends in our knowledge of bacterial adaptation to quinolone antibiotics is described. This is followed by point mutagenesis in eukaryotic genomes, going from drug resistance in malaria to the nefarious effects of cigarette smoking. Finally, two contemporary synthetic point mutagenesis methodologies are described. Colin Logie Nijmegen Centre of Molecular Life Sciences, Nijmegen, The Netherlands [...]... of point mutations: nucleotide replacements produced by the genomic and snp mutations and replication slippage events There are several possible realizations of mutation density studies One can look for the differences between genomic and snp nucleotide replacements and replication slippage mutations Further, one can compare the mutation densities occurring in the human genome to those 18 Point Mutation. ..Part 1 Current Views on Point Mutation Theory 1 Point Mutations, Their Transition Rates and Involvements in Human and Animal Disorders Viliam Šnábel Parasitological Institute, Slovak Academy of Sciences, Košice, Slovakia 1 Introduction Point mutation or single base substitution is the replacement of a single base nucleotide with another nucleotide of the genetic material Point mutations can be divided... programmed cell death (BirchMachin, 2006) The first primary pathological mutations in mtDNA were discovered over 20 years ago (Holt et al., 1988; Wallace et al., 1988), and since then more than 100 mutations of mtDNA have been linked to human disease The vast majority of these mutations fall into 6 Point Mutation two classes: point mutations and large-scale rearrangements The latter can be partial deletions... time by TpG/CpAs Mammals thus exhibit two dramatically different neutral mutation rates: the CpG mutation rate and the non-CpG rate Walser et al (2011) determined the neutral non-CpG mutation rate as a function of CpG content by comparing sequence divergence of thousands of pairs of neutrally evolving chimpanzee and human orthologs that differ primarily in CpG content Both the mutation rate and the mutational... 2008) Pan et al (2011) identified 8 Point Mutation heat-shock protein 60 (HSP 60) as one of the most frequently expressed biomolecules after albendazole treatment of patients that could be connected with beta-tubulin gene isoform 2 which exhibits a conserved point mutation indicative of benzimidazole resistance in tapeworm Echinococcus granulosus Detection of point mutations has been beneficial in allowing... Microsatellite markers exhibit mutation rates that exceed the average mutation rates by two orders of magnitude In this work we shall put under scrutiny whether the nucleotide replacement process and the replication slippage mechanism produce comparable densities of mutational changes 1.4 The distribution of mutations along the chromosomes Since stochasticity is an essential component of the mutational processes... affected by an OXPHOS defect due to nuclear or mtDNA mutations were observed Patients with nuclear mutations became symptomatic at a young age, and had a severe clinical course Patients with mtDNA mutations showed a wider clinical spectrum of age at onset and severity Reported differences are of importance regarding the choice of type of genome in further studies of affected patients 2.2 Point mutations... with widely varying base composition exhibit uniformity of transition mutation rate both within and among mammalian lineages, with no relationship to intrachromosomal or interchromosomal effects This points to similarity in point mutation processes in genomic regions with substantially different GCcontent biases Knowledge of the mutational transition/transversion rate bias also allows a prediction... range of species by postulating that the production of intracellular ROS is the major determinant of life span Intracellular ROS are primarily generated by the mitochondrial respiratory chain and thus constitute a prime target for oxidative damage According to this theory, mtDNA mutations caused by ROS accumulate within the cell, leading to impaired respiratory chain proteins, thereby generating more... are encoded by both nuclear and mitochondrial genes Therefore, Rubio-Gozalbo et al (2000) examined whether there are clinical differences in patients suffering from OXPHOS defects caused by nuclear or mtDNA mutations 16 families with >=2 two siblings bearing a genetically established OXPHOS deficiency were studied, in four families due to a nuclear gene mutation and twelve due to a mtDNA mutation Differences . POINT MUTATION Edited by Colin Logie Point Mutation Edited by Colin Logie Published by InTech Janeza Trdine. Point Mutation, Edited by Colin Logie p. cm. ISBN 978-953-51-0331-8 Contents Preface IX Part 1 Current Views on Point Mutation