Nucleic Acids â#x80;#x93; From Basic Aspects to Laboratory Tools

This edited book, "Nucleic Acids - From Basic Aspects to Laboratory Tools", contains a series of chapters that highlight the development and status of the various aspects of the nucleic acids related to DNA chemistry and biology and the molecular application of these small DNA molecules and related synthetic analogues within biological systems. Furthermore, it is hoped that the information in the present book will be of value to those directly engaged in the handling and use of nucleic acids, and that this book will continue to meet the expectations and needs of all who are interested in the different fascinating aspects of molecular biology. ave4eva 2016 Cover 1 Nucleic Acids: From Basic Aspects to Laboratory Tools 2 © 3 Contents 5 Preface 8 Chapter 1 Nucleic Acid Isolation and Downstream Applications 10 1. Introduction 10 1.1. Nucleic acid isolation and downstream applications 10 2. Nucleic acid extraction methods 11 3. Nucleic acid and Restriction Enzyme Analysis (REA) 17 4. Nucleic acid detection 18 5. Nucleic acid identification by sequencing methods 26 5.1. Next-Generation Sequencing (NGS) platforms 28 5.2. Illumina sequencing by synthesis 28 5.3. Nanopore technology 30 Author details 31 References 31 Chapter 2 Nucleic Acids Extraction from Formalin-Fixed and Paraffin-Embedded Tissues 36 1. Introduction 36 2. Factors affecting nucleic acids extraction from FFPE tissues 37 3. Preparing FFPE tissue sections for nucleic acids extraction 39 4. RNA extraction from FFPE tissues 40 4.1. Evaluating RNA concentration and quality 41 4.2. Results and comments on the herein described RNA extraction protocols 41 5. DNA extraction from FFPE tissues 42 5.1. DNA quality quantification and analysis 43 5.2. Results and comments on the herein described DNA extraction protocols 43 Author details 44 References 44 Chapter 3 Nucleic Acid Detection of Major Foodborne Viral Pathogens Human: Noroviruses and Hepatitis A Virus 46 1. Introduction 46 2. Key notes from norovirus and hepatitis A virus 47 2.1. Norovirus genome and molecular diversity 47 2.2. HAV genome and genotypes 48 3. Nucleic acid-based detection 49 3.1. Direct nucleic acid probe hybridization 49 3.2. Nucleic acid amplification 49 3.2.1. Reverse transcription-PCR 50 3.2.2. Quantitative real time RT-PCR (RT-qPCR) 51 References 52 References 53 3.3. Nucleic acid amplification coupled with DNA microarray detection 55 3.4. Detection of infectious viruses 56 4. Concluding remarks 56 Author details 57 References 57 Chapter 4 Nucleic Acid-based Diagnosis and Epidemiology of Infectious Diseases 68 1. Introduction 69 1.1. Diagnosis 69 1.1.1. Nucleic acid detection methods 70 1.1.2. Advantages and drawbacks of single and multiple copy genes 71 1.1.3. Identification of drug resistance 72 1.2. Epidemiology 72 1.2.1. Classic genotyping and next-generation sequencing methods 73 1.2.2. Genetic variability and its impact on pathology and virulence 74 1.2.3. Disease control and vaccines 75 2. Final Considerations 76 Author details 76 References 77 Chapter 5 Nucleic Acids — The Use of Nucleic Acid Testing in Molecular Diagnostics 84 1. Introduction 84 2. Nucleic acid detection in molecular diagnostics 86 2.1. The importance of nucleic acid measurement for HIV-1 86 2.2. Other therapeutic areas 90 2.2.1. Microbiology and infectious diseases 90 2.2.2. Blood screening 91 2.2.3. Human genetics—Testing via nucleic acid markers 91 2.2.3.1. Prenatal diagnosis 91 2.2.3.2. Inherited diseases 92 2.2.3.3. Cancer markers 93 3. Conclusion and a future outlook 94 Author details 95 References 95 Chapter 6 Application of Nucleic Acid Aptamers to Viral Detection and Inhibition 102 1. Introduction 102 2. Aptamers against viruses 104 2.1. Aptamers against Rous Sarcoma Virus (RSV) 104 2.2. Aptamers against Human Immunodeficiency Virus type I (HIV-1) 105 2.2.1. Aptamers against HPV 108 2.3. Aptamers against influenza virus 111 2.3.1. Influenza A Virus (IAV) 111 2.3.2. Influenza B Virus (IVB) 114 2.4. Aptamers against HCV 114 3. Aptamer structures 118 4. Challenges for aptamer technology 119 5. Conclusion 120 Author details 120 References 121 Chapter 7 DNA G-Quadruplex as a Reporter System for Sensor Development 130 1. Introduction 130 2. Basic structures of DNA G-quad 131 3. G-quad mimicking peroxidase activity in colorimetric-based sensors 132 4. G-quad as fluorescence probes 135 5. G-quad in luminescence-based sensors 137 6. G-quad integrates with electrochemistry 138 7. G-quad integrates with quantum dots 140 8. Conclusion 141 Author details 142 References 142 Chapter 8 Small-molecule Nucleic-acid-based Gene-silencing Strategies 146 1. Introduction 146 2. DNAzymes 147 2.1. The possible mechanisms and characteristics of DNAzymes 147 2.2. DNAzymes delivery systems – Past to present 148 2.3. Application of DNAzymes in vivo and in vitro 148 2.4. DNAzymes in clinical trials 150 3. Small interfering RNA 152 3.1. The possible mechanisms and challenges of siRNAs 152 3.2. SiRNAs delivery systems 153 3.3. Application of siRNAs – From the bench to the clinic 154 4. Antisense oligonucleotides 155 5. Ribozymes 156 6. Aptamers 157 7. Decoys 157 8. Concluding remarks 158 Author details 158 References 158 Chapter 9 Temperature-Dependent Regulation of Bacterial Gene Expression by RNA Thermometers 166 1. Introduction 166 2. Molecular mechanism underlying the regulatory function of RNA thermometers 168 3. Identification of RNA thermometers 169 3.1. In silico predictions 169 3.2. Identification with experimental approaches 170 3.3. RNA structuromics 172 4. Families of RNA thermometers 173 4.1. ROSE-like RNA thermometers 174 4.2. FourU RNA thermometers 175 4.3. Additional types of RNA thermometers 177 5. Bacterial processes controlled by RNA thermometers 179 5.1. Heat shock response 179 5.2. Virulence-associated genes of pathogenic bacteria 180 6. Future directions 181 7. Nomenclature 185 Author details 186 References 186 Chapter 10 A Review on the Thermodynamics of Denaturation Transition of DNA Duplex Oligomers in the Context of Nearest-Neighbor Models 192 1. Introduction 192 2. A quantum mechanics formulation for sequence properties 195 3. Nucleotide class-state representation 195 4. Irreducible representation 197 4.1. Double strands 199 5. The modeling based on end effects 201 6. Results and discussion for the modeling based on the end effects 203 7. The modeling based on double helix initiation parameters 206 8. Results and discussion for the modeling based on double helix initiation parameters 213 9. Conclusions 216 Author details 217 References 217 Спизжено у ExLib: avxhome.se/blogs/exLib (Stole src from http://avxhome.se/blogs/exLib): tanas.olesya (avax); Snorgared,D3pZ4i & bhgvld,Denixxx (for softarchive) My gift to leosan==leonadin GasGeo&BioMedLover from ru-board :-) Спизжено у ExLib: avxhome.se/blogs/exLib (Stole src from http://avxhome.se/blogs/exLib):,tanas.olesya (avax),Snorgared,D3pZ4i & bhgvld,Denixxx,(for softarchive),My gift to leosan==leonadin GasGeo&BioMedLover from ru-board :-) Chapter 1 Nucleic Acid Isolation and Downstream Applications by Ivo Nikolaev Sirakov Chapter 2 Nucleic Acids Extraction from Formalin-Fixed and Paraffin-Embedded Tissues by Gisele R. Gouveia, Suzete C. Ferreira, Sheila A. C. Siqueira and Juliana Pereira Chapter 3 Nucleic Acid Detection of Major Foodborne Viral Pathogens: Human Noroviruses and Hepatitis A Virus by Haifeng Chen Chapter 4 Nucleic Acid-based Diagnosis and Epidemiology of Infectious Diseases by Márcia Aparecida Sperança, Rodrigo Buzinaro Suzuki, Aline Diniz Cabral and Andreia Moreira dos Santos Carmo Chapter 5 Nucleic Acids — The Use of Nucleic Acid Testing in Molecular Diagnostics by Gabrielle Heilek Chapter 6 Application of Nucleic Acid Aptamers to Viral Detection and Inhibition by Ana Gabriela Leija-Montoya, María Luisa Benítez-Hess and Luis Marat Alvarez-Salas Chapter 7 DNA G-Quadruplex as a Reporter System for Sensor Development by Qiuting Loh and Theam Soon Lim Chapter 8 Small-molecule Nucleic-acid-based Gene-silencing Strategies by Zhijie Xu and Lifang Yang Chapter 9 Temperature-Dependent Regulation of Bacterial Gene Expression by RNA Thermometers by Yahan Wei and Erin R. Murphy Chapter 10 A Review on the Thermodynamics of Denaturation Transition of DNA Duplex Oligomers in the Context of Nearest-Neighbor Models by João C. O. Guerra

This book on Acrylic Polymers for Healthcare presents eight chapters organised into three parts by providing new ideas in design, synthesis and a detailed study of new acrylate materials in healthcare applications. Part I represents Chapters 1, 2, 3 and 4 focussing on toning up of technologies for making dental dentures with better properties. Part II comprises Chapters 5 and 6 dealing with synthetic polymer-based nanoparticles as intelligent drug delivery systems and bismuth nanoparticles for improved green light emission. Part III represents Chapters 7 and 8 describing the aspects of mitigation of acrylamide in foods in the context of an African perspective and the importance of acrylic-based polymeric adsorbents so that the reader can get an idea about the various types and forms of polymeric materials used for the removal of heavy metals from water.

Human noroviruses (hNoVs) and hepatitis A virus (HAV) are the leading cause of foodborne viral illness, and they exact a considerable economic and health toll worldwide. The detection of viral contamination in foods requires highly sensitive and accurate methods, due to the intrinsically low amounts of viruses and the complexity of the sample matrices. In recent years, a wide variety of nucleic acid-based molecular methods have been developed for the detection of hNoVs and HAV, displaying superior sensitivity, specificity, and speed. This chapter aims to provide a summary of the application of the molecular methods for the detection of the two important foodborne viruses