Extracellular Nucleic Acids (eBook)

Preface 6
Contents 8
Contributors 10
Chapter 1: Extracellular DNA as Matrix Component in Microbial Biofilms 14
1.1 Introduction 15
1.2 Extracellular DNA as Matrix Component in P. aeruginosa Biofilm 16
1.3 Extracellular DNA as Matrix Component in Streptococcal Biofilm 19
1.4 Extracellular DNA as Matrix Component in Staphylococcal Biofilm 21
1.5 Final Remarks 23
References 23
Chapter 2: Gene Transfer Agents and Defective Bacteriophages as Sources of Extracellular Prokaryotic DNA 28
2.1 Viruses in the Environment and Packaging of Host DNA 28
2.2 Defective Phages and Extracellular DNA 30
2.3 Gene Transfer Agents and Extracellular DNA 31
2.4 Concluding Remarks 34
References 35
Chapter 3: Roles of Extracellular DNA in Bacterial Ecosystem 38
3.1 Extracellular DNA in Natural Environments 39
3.2 Extracellular DNA as Nutrient 40
3.3 Extracellular DNA as Genetic Material 40
3.4 Extracellular DNA in Biofilm 41
3.5 Uptake and Release of DNA 43
3.6 Uptake of Extracellular DNA by Indigenous Bacteria 47
References 48
Chapter 4: Stable Extracellular DNA: A Novel Substrate for Genetic Engineering that Mimics Horizontal Gene Transfer in Nature 51
4.1 Introduction 52
4.1.1 Transformable Recipient Microorganisms 53
4.1.2 Natural Transformation Demonstrated in the Laboratory Test-tube 54
4.1.3 Why Is Natural Transformation Important for Molecular Biology Research and Application? 55
4.2 Production of Stable Extracellular DNA Released from Donor Cells 56
4.2.1 Extracellular DNAs Released from Cells Lysed in the Laboratory 56
4.2.2 Extracellular DNA: An Active Substrate in the Natural Transformation of a Gram-Positive Bacterium 58
4.3 Engineered Natural Transformation in the Laboratory 60
4.3.1 Integration of Extracellular DNA into the Engineered Recipient Genome 60
4.3.2 Integration of 100kb DNA into B. subtilis by the CMM 61
4.4 Conclusions and Future Perspectives 61
References 63
Chapter 5: Extracellular Nucleic Acids of the Marine Phototrophic Bacterium Rhodovulum sulfidophilum and Related Bacteria: Physiology and Biotechnology 66
5.1 Introduction 67
5.2 Flocculation and Extracellular Nucleic Acid Production 67
5.2.1 Rhodovulum sp. Strain PS88 67
5.2.2 Extracellular DNA and Flocculation of Rhodovulum sulfidophilum 69
5.2.3 DNA as the Cell-to-Cell Interconnecting Compound in Floc of Rdv. sulfidophilum 71
5.3 Analysis of Extracellular Nucleic Acids 72
5.3.1 Extracellular RNAs of Rdv. sulfidophilum 72
5.3.2 Extracellular DNA of Rdv. sulfidophilum 73
5.3.3 Mechanism for Release of Extracellular DNA and RNA of Rdv. sulfidophilum 73
5.4 Biotechnology 74
5.4.1 Utility as a Nucleotide Source 74
5.4.2 RNA Drug Production by Engineered Plasmids 74
References 76
Chapter 6: Systemic RNAi in C. elegans from the Viewpoint of RNA as Extracellular Signals 79
6.1 Introduction 80
6.2 Systemic RNAi and Trafficking Pathways Associated with Method of Delivery 80
6.2.1 Systemic and Heritable Nature of RNAi in Response to Injected dsRNA 82
6.2.2 Systemic Nature of RNAi in Response to Transgene Delivery of dsRNA 83
6.2.3 Systemic RNAi in Response to Ingestion of dsRNA 85
6.3 RNA Silencing Mechanisms in C. elegans 85
6.3.1 The Nature of Silencing Molecules in C. elegans 88
6.3.1.1 RNA Silencing Molecules Associated with Experimental Delivery of dsRNA 88
6.3.1.2 Endogenous Silencing RNAs and Associated RNA Silencing Mechanisms 89
6.3.2 Mechanisms that Inhibit RNAi Responses 92
6.3.3 Mechanisms that Facilitate Spreading of RNA Silencing Molecules 93
6.3.3.1 Endocytosis 94
6.3.3.2 Transmembrane Proteins 96
6.4 Conclusions 98
References 99
Chapter 7: Circulating Nucleic Acids in Health and Disease 103
7.1 Introduction 104
7.2 Circulating NA in Cancer 104
7.2.1 Genomic and Mitochondrial DNA Mutations 105
7.2.2 Microsatellite Alterations 109
7.2.3 Aberrant DNA Methylation in Cancer 110
7.2.4 Viral DNA in the Circulation 116
7.2.5 Tumor-Associated mRNA Detection in Blood 117
7.2.6 CirNA Elevated Levels in Cancer 118
7.2.7 DNA and RNA Integrity 119
7.2.8 Technical Aspects of cirNA Detection 120
7.3 Circulating Nucleic Acids in Other Diseases 121
7.3.1 CirNA in Diabetes Mellitus 121
7.3.2 Trauma and Acute Diseases 122
7.3.3 Exhaustive Exercise 123
7.3.4 Acute Myocardial Infarction 123
7.3.5 Stroke 123
7.3.6 Transplantation 124
7.3.7 Sickle Cell Disease 125
7.4 Potential Therapeutic Implications of the cirNA 125
7.5 Conclusion 126
References 127
Chapter 8: Circulating MicroRNAs in Cancer 139
8.1 MicroRNAs: History, Biogenesis, and Mechanism of Action 140
8.2 Tumor Cell miRNAs in Cancer Biology and as Tissue-Based Disease Biomarkers 141
8.3 Circulating MicroRNAs as a Novel Class of Blood-Based Biomarker for Cancer Detection: Potential Utility and Current Challenges 142
8.4 Circulating MicroRNAs: Biological Mechanisms 150
8.5 Concluding Remarks 153
References 153
Chapter 9: Biology and Diagnostic Applications of Cell-Free Fetal Nucleic Acids in Maternal Plasma 156
9.1 Introduction 157
9.2 From Circulating Fetal Cells to Circulating Fetal Nucleic Acids 157
9.3 Characteristics of Circulating Fetal Nucleic Acids in Maternal Plasma 158
9.4 Origin of Circulating Fetal Nucleic Acids 159
9.5 Clinical Application of Circulating Fetal Nucleic Acids 161
9.5.1 Qualitative Analysis of Circulating Fetal Nucleic Acids 161
9.5.2 Quantitative Analysis of Circulating Fetal Nucleic Acids 165
9.5.3 The Development of Universal Fetal Markers 165
9.5.4 Chromosomal and Allelic Dosage Analysis 167
9.5.5 Enrichment of Circulating Fetal Nucleic Acids in Maternal Plasma 169
9.5.6 Preanalytical Issues in Circulating Fetal Nucleic Acid Analysis 170
9.6 Conclusion and Speculation 170
References 171
Chapter 10: The Biology of Circulating Nucleic Acids in Plasma and Serum (CNAPS) 176
10.1 Introduction 177
10.2 Nucleic Acid and Nuclease Content 178
10.3 Nucleic Acid Sources 179
10.3.1 DNA 179
10.3.1.1 Leucocytes 179
10.3.1.2 Bacteria and Viruses 179
10.3.1.3 Cell-Surface DNA 180
10.3.1.4 Necrosis 180
10.3.1.5 Apoptosis 180
10.3.1.6 Exosomes 181
10.3.1.7 Spontaneously Released, Newly Synthesized DNA 181
10.3.2 RNA 182
10.3.2.1 Leucocytes 182
10.3.2.2 Bacteria and Viruses 182
10.3.2.3 Necrosis and Apoptosis 182
10.3.2.4 Exosomes 183
10.3.2.5 Spontaneous Released, Newly Synthesised RNA 183
10.4 Origin and Timing of Nucleic Acid Release 184
10.4.1 DNA 184
10.4.2 RNA 185
10.5 Released Nucleic Acids Can Enter and Express in Other Cells 185
10.5.1 DNA 185
10.5.1.1 Released Prokaryote DNA Enters Eukaryote Cells 185
10.5.1.2 Release and Uptake of DNA by Eukaryote Cells 186
10.5.2 RNA 189
10.6 Mechanisms of CNAPS Entry into CELLS 189
10.6.1 DNA Entry into Mouse Skeletal Muscle 189
10.6.2 DNA Entry into Human Keratinocytes 190
10.6.3 DNA Entry into Mouse (Leukaemia) J774 Cells 190
10.6.4 dsRNA Entry into Murine GEnC Cells 191
10.6.5 RNA Entry into ECV304 Cells 191
10.6.6 Viral RNA Entry into 2B2318 Lymphocytes 191
10.7 Conclusions 192
References 192
Chapter 11: Modulation and Regulation of Gene Expression by CpG Oligonucleotides 199
11.1 Introduction 200
11.2 Modulation and Regulation of Gene Expression by CpG ODN In vitro 201
11.2.1 Gene Expression Studies Involving a Single Cell Type In vitro 201
11.2.2 Gene Expression Studies with Mixed Cell Populations In vitro 202
11.2.3 Temporal Activation of Genes in the TLR9 Signaling Pathway 202
11.2.4 Regulatory Networks Triggered by CpG DNA Stimulation In Vitro 204
11.3 Modulation and Regulation of Gene Expression by CpG ODN In vivo 206
11.3.1 Regulatory Networks Underlying CpG-Dependent Gene Expression In vivo 206
11.3.2 Temporal Pattern of Gene Upregulation Mediated by TLR9 Engagement 208
11.3.3 Mechanism of Downregulation of CpG Induced Gene Expression 209
11.4 Synergistic Modulation and Regulation of Gene Expression by TLR3 and TLR9 Ligands 210
11.4.1 Genome-Wide Changes in Gene Expression After CpG ODN and Poly (I:C) Treatment 211
11.4.2 Regulatory Networks Triggered by CpG ODN Vs. Poly (I:C) 212
11.4.3 Genes Synergistically Upregulated by Co-administration of CpG ODN and Poly (I:C) 213
References 213
Chapter 12: Immune Recognition of Nucleic Acids and Their Metabolites 217
12.1 Introduction 218
12.2 The Fundamental Mechanism to Avoid False Recognition of Harmless Nucleic Acids: The Case of Food Metabolism 218
12.3 The Mechanism to Distinguish Healthy ``Self´´ Nucleic Acids 219
12.3.1 The Mechanism to Detect Exogenous Nucleic Acids Breaking into Host Cells: The Case of Microbial Infections 220
12.3.1.1 Endosomal Recognition for Exogenous Nucleic Acids via TLRs 221
12.3.1.2 Cytoplasmic Sensors for Exogenous Nucleic Acids 223
12.3.2 The Mechanism to Avoid the False Recognition of the Endogenous Nucleic Acids: The Case of Tissue Damage 225
12.3.3 The Mechanism to Recognize Endogenous Nucleic Acids and Their Metabolites as Danger Signal: Another Case of Tissue Damage 226
12.3.4 Endogenous Nucleic Acids Recognition: The Case of Autoimmune Diseases 227
12.4 Therapeutic Applications of Nucleic Acids as Innate Immune Activators: Vaccine and Vaccine Adjuvants (Table12.2) 228
12.5 Conclusions 230
References 230
Index 236