Front Cover -- Insect Molecular Genetics -- Copyright Page -- Contents -- Preface to the Third Edition -- Preface to the Second Edition -- Preface to the First Edition -- Goals -- Organization -- Acknowledgments -- I: GENES AND GENOME ORGANIZATION IN EUKARYOTES -- 1 DNA, Gene Structure, and DNA Replication -- 1.1 Overview -- 1.2 DNA is the Hereditary Material: A Brief History -- 1.3 The Central Dogma -- 1.4 The "RNA World" Came First? -- 1.5 The Molecular Structure of DNA -- 1.6 The Molecular Structure of RNA -- 1.7 The Double Helix -- 1.8 Complementary Base Pairing is Fundamental -- 1.9 DNA Exists in Several Forms -- 1.10 Genes -- 1.11 The Genetic Code for Protein-Coding Genes is a Triplet and is Degenerate -- 1.12 Gene Organization -- 1.13 Efficient DNA Replication is Essential -- 1.14 DNA Replication is Semiconservative -- 1.15 Replication Begins at Replication Origins -- 1.16 DNA Replication Occurs Only in the 5' to 3' Direction -- 1.17 Replication of DNA Requires an RNA Primer -- 1.18 Ligation of Replicated DNA Fragments -- 1.19 DNA Replication during Mitosis in Eukaryotes -- 1.20 Telomeres at the End: A Solution to the Loss of DNA during Replication -- 1.21 DNA Replication Fidelity and DNA Repair -- 1.22 Mutations in the Genome -- 1.23 Common Genetic Terminology -- 1.24 Independent Assortment and Recombination during Sexual Reproduction -- General References -- References Cited -- 2 Transcription, Translation, and Regulation of Eukaryotic DNA -- 2.1 Overview -- 2.2 Introduction -- 2.3 RNA Synthesis is Gene Transcription -- 2.4 Transcription Involves Binding, Initiation, Elongation, and Termination -- 2.5 RNA Transcripts of Protein-Coding Genes -- 2.6 RNA of Protein-Coding Genes Must Be Modified and Processed in Eukaryotes -- 2.7 Splicing Out the Introns -- 2.8 Translation Involves Protein Synthesis -- 2.9 RNA Surveillance: Damage Control.

2.10 Import and Export from the Nucleus -- 2.11 Transport of Proteins within the Cytoplasm -- 2.12 mRNA Stability -- 2.13 Chaperones and the Proteosome -- 2.14 RNA Silencing or Interference and miRNAs -- 2.15 Gene Regulation in Eukaryotes -- 2.16 Insulators and Boundaries -- 2.17 Chromosome or Gene Imprinting in Insects -- 2.18 Eukaryotic Genomes and Evolution -- References Cited -- 3 Nuclear and Extranuclear DNA in Insects -- 3.1 Overview -- 3.2 Introduction -- 3.3 C-Value Paradox: Is it Real? -- 3.4 Repetitive DNA is Common in Insects -- 3.5 Composition of Insect DNA -- 3.6 Chromosomes are DNA Plus Proteins -- 3.7 Packaging Long, Thin DNA Molecules into Tiny Spaces -- 3.8 Structure of the Nucleus -- 3.9 Euchromatin and Heterochromatin -- 3.10 Centromeres -- 3.11 Telomeres -- 3.12 Chromosomes during Mitosis and Meiosis -- 3.12.1 Mitosis -- 3.12.2 Meiosis -- 3.13 Chromosome Damage -- 3.14 Polyteny -- 3.15 Chromosomal Puffing -- 3.16 B Chromosomes -- 3.17 Sex Chromosomes -- 3.18 Extranuclear Inheritance in Mitochondrial Genes -- 3.19 Transposable Elements are Ubiquitous Agents that Alter Genomes -- References Cited -- 4 Genetic Systems, Genome Evolution, and Genetic Control of Embryonic Development in Insects -- 4.1 Overview -- 4.2 Introduction -- 4.3 Genetic Systems in Insects -- 4.4 Endopolyploidy is Common in Somatic Tissues of Arthropods -- 4.5 Genetics of Insects Other than D. melanogaster -- 4.6 Dynamic Insect Genomes -- 4.6.1 Horizontal Gene Transfer from Microorganisms to Insects -- 4.7 B Chromosomes -- 4.8 Unique-Sequence DNA in the Nucleus -- 4.9 Middle-Repetitive DNA in the Nucleus -- 4.9.1 Heat-Shock Genes -- 4.9.2 Histone Genes -- 4.9.3 Immune-Response Genes -- 4.9.4 Ribosomal Genes -- 4.9.5 Silk Genes -- 4.9.6 Transfer RNA Genes -- 4.9.7 Vitellogenin Genes -- 4.9.8 Transposable Elements -- 4.10 Highly Repetitive DNA.

4.11 Producing Large Amounts of Protein in a Short Time: Gene Amplification and Gene Duplication -- 4.11.1 Chorion Genes in Drosophila and Moths -- 4.11.2 Insecticide Resistance -- 4.12 Multiple Genomes in or on Insects: What is the "Biological Individual"? -- 4.12.1 Multiple Symbionts -- 4.12.2 Wolbachia and Cardinium -- 4.12.3 Polydnaviruses in Parasitoids -- 4.12.4 Gut Symbionts in Arthropods -- 4.12.4.1 Termite and Cockroach Symbionts -- 4.12.4.2 Rhagoletis Symbionts -- 4.12.5 Symbiosis in Fungus-Growing Attine Ants -- 4.12.6 Southern Pine Beetle Symbionts -- 4.12.7 Aphid Symbionts -- 4.12.8 Tsetse Fly Symbionts -- 4.13 Insect Development -- 4.13.1 Oocyte Formation in D. melanogaster -- 4.13.2 Embryogenesis in D. melanogaster -- 4.13.3 Postembryonic Development -- 4.14 Dissecting Development with D. melanogaster Mutants -- 4.14.1 Maternal-Effect Genes -- 4.14.2 Zygotic-Segmentation Genes -- 4.14.2.1 Gap Genes -- 4.14.2.2 Pair-Rule Genes -- 4.14.2.3 Segment-Polarity Genes -- 4.14.2.4 Homeotic Genes -- 4.14.3 Insect Metamorphosis -- 4.15 Interactions During Development -- 4.16 Similarities and Differences in Development in Other Insects -- 4.17 Evo-Devo and the Revolution in Developmental Studies -- References Cited -- II: MOLECULAR GENETIC TECHNIQUES -- 5 Some Basic Tools: How to Cut, Paste, Copy, Measure, Visualize, and Clone DNA -- 5.1 Overview -- 5.2 Introduction to a Basic Molecular Biology Experiment -- 5.2.1 The Pros and Cons of Kits -- 5.2.2 A Simple Cloning Experiment -- 5.3 Extracting DNA from Insects -- 5.3.1 DNA Extraction Resulting in Loss of the Specimens -- 5.3.2 DNA Extraction That Does Not Require Destroying the Specimens -- 5.3.3 Assessing the Quality of Extracted DNA -- 5.4 Precipitating Nucleic Acids -- 5.5 Shearing DNA -- 5.6 Cutting DNA with Restriction Endonucleases -- 5.7 Joining DNA Molecules.

5.8 Growth, Maintenance, and Storage of E. coli -- 5.9 Plasmids for Cloning in E. coli -- 5.10 Transforming E. coli with Plasmids -- 5.11 Purifying Plasmid DNA from E. coli -- 5.12 Electrophoresis in Agarose or Acrylamide Gels -- 5.13 Detecting, Viewing, and Photographing Nucleic Acids in Gels -- 5.14 Identifying Specific DNA by Southern Blot Analysis -- 5.15 Labeling DNA or RNA Probes -- 5.16 Removing DNA from Agarose Gels after Electrophoresis -- 5.17 Restriction-Site Mapping -- General References -- References Cited -- 6 Some Additional Tools for the Molecular Biologist -- 6.1 Overview -- 6.2 Introduction -- 6.3 The Perfect Genomic Library -- 6.3.1 Lambda (λ) Phage as a Vector -- 6.3.2 Cloning with Cosmids -- 6.3.3 Cloning in the Filamentous Phage M13 -- 6.3.4 Phagemids -- 6.3.5 BACs -- 6.4 cDNA Cloning -- 6.5 Enzymes Used in Molecular Biology Experiments -- 6.6 Isolating a Specific Gene from a Library if Whole-Genome Sequencing is Not Done -- 6.7 Labeling Probes by a Variety of Methods -- 6.7.1 Synthesis of Uniformly Labeled DNA Probes by Random Primers -- 6.7.2 Synthesis of Probes by Primer Extension -- 6.7.3 End-Labeled Probes -- 6.7.4 Single-Stranded Probes -- 6.7.5 Synthetic Probes -- 6.8 Baculovirus Vectors Express Foreign Polypeptides in Insect Cells -- 6.9 Expression Microarray Analysis -- General References -- References Cited -- 7 DNA Sequencing and the Evolution of the "-Omics" -- 7.1 Overview -- 7.2 Introduction -- 7.3 The Dideoxy or Chain-Termination (Sanger) Method -- 7.4 The Maxam and Gilbert Sequencing Method -- 7.5 Shotgun Strategies for Genomes -- 7.6 Sequencing DNA by the Polymerase Chain Reaction (PCR) -- 7.7 Automated Sanger Sequencers -- 7.7.1 Decreasing Costs of Sanger Sequencing -- 7.8 Analyzing DNA Sequence Data -- 7.9 DNA-Sequence Data Banks -- 7.10 A Brief History of the Drosophila Genome Project.

7.10.1 The Original Drosophila Genome Project -- 7.10.2 The Actual Drosophila Genome Project -- 7.10.3 Drosophila Genome Analysis -- 7.10.4 Surprises in the Drosophila Genome -- 7.11 Next-Generation Sequencing Methods and Beyond -- 7.11.1 Next-Generation (NextGen or Second-Generation) Sequencing -- 7.11.1.1 Roche (454) GS FLX Sequencer -- 7.11.1.2 Illumina (or Solexa) Genome Analyzer -- 7.11.1.3 Applied Biosystems SOLiD Sequencer -- 7.11.1.4 Standards -- 7.11.2 Third-Generation Sequencing -- 7.12 Bioinformatics -- 7.12.1 Gene Ontology -- 7.13 Genome Analyses of Other Arthropods -- 7.13.1 Interesting Findings from Completed Genomes -- 7.13.2 What Do You Need to Do to Sequence Your Favorite Insect's Genome? -- 7.14 Transposable Elements (TEs) as Agents of Genome Evolution -- 7.15 Transcriptomics -- 7.15.1 Tiling Microarrays -- 7.16 Metagenomics -- 7.17 Proteomics: Another "-Omic" -- 7.18 Functional Genomics -- 7.19 Structural Genomics-Another New Horizon? -- 7.20 Comparative Genomics -- 7.21 Interactomes or Reactomes -- 7.22 The Post-Genomic Era: Systems Genetics -- General References -- References Cited -- 8 DNA Amplification by the Polymerase Chain Reaction: Molecular Biology Made Accessible -- 8.1 Overview -- 8.2 Introduction -- 8.3 The Basic Polymerase Chain Reaction (PCR) -- 8.3.1 The First Few Cycles are Critical -- 8.3.2 PCR Power -- 8.3.3 Standard PCR Protocols -- 8.3.4 DNA Polymerases -- 8.3.5 Other Thermostable DNA Polymerases -- 8.3.6 Primers are Primary -- 8.3.7 Storing Insects for the PCR -- 8.3.8 Preparing DNA Samples -- 8.3.9 PCR Automation -- 8.3.10 Specificity of the PCR -- 8.3.11 Detecting Primer Artifacts -- 8.3.12 How Many Cycles Does a PCR Need? -- 8.3.13 Reducing the Evils of Contamination -- 8.4 Some Modifications of the PCR -- 8.4.1 AFLP for DNA Fingerprinting -- 8.4.2 Anchored PCR -- 8.4.3 Arbitrary Primers.

8.4.4 Asymmetric PCR.