Chapter
1.4. The ``RNA World´´ Came First?
1.5. The Molecular Structure of DNA
1.6. The Molecular Structure of RNA
1.8. Complementary Base Pairing is Fundamental
1.9. DNA Exists in Several Forms
1.11. The Genetic Code for Protein-Coding Genes is a Triplet and is Degenerate
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
Chapter 2: Transcription, Translation, and Regulation of Eukaryotic DNA
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
2.13. Chaperones and the Proteasome
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
Chapter 3: Nuclear and Extranuclear DNA in Insects
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
3.12. Chromosomes During Mitosis and Meiosis
3.15. Chromosomal Puffing
3.18. Extranuclear Inheritance in Mitochondrial Genes
3.19. Transposable Elements (TEs) Are Ubiquitous Agents That Alter Genomes
Chapter 4: Genetic Systems, Genome Evolution, and Genetic Control of Embryonic Development in Insects
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 (HGT) From Microorganisms to Insects
4.8. Unique-Sequence DNA in the Nucleus
4.9. Middle-Repetitive DNA in the Nucleus
4.9.3. Immune-Response Genes
4.9.6. Transfer RNA (tRNA) Genes
4.9.7. Vitellogenin Genes
4.9.8. Transposable Elements (TEs)
4.10. Highly Repetitive DNA
4.11. Producing Large Amounts of Protein 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 Attine Fungus-Growing Ants
4.12.6. Southern Pine Beetle Symbionts
4.12.8. Tsetse Fly Symbionts
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
4.14.2.2. Pair-Rule Genes
4.14.2.3. Segment-Polarity Genes
4.14.3. Insect Metamorphosis
4.15. Interactions During Development
4.16. Similarities and Differences in Development in Other Insects
4.16.1. Development in Other Insects
4.17. Evo-Devo and the Revolution in Developmental Studies
Part II: Molecular Genetic Techniques
Chapter 5: Some Basic Tools: How to Isolate, Cut, Paste, Copy, Measure, Visualize, and Clone DNA
5.2. Introduction to a Basic Molecular Biology Experiment
5.2.1. A Simple Cloning Experiment
5.2.2. The Pros and Cons of Kits
5.3. Extracting DNA From Insects
5.3.1. DNA Extraction Resulting in Loss of Specimens
5.3.2. DNA Extraction That Does Not Destroy the Specimen
5.3.3. Assessing Quality of Extracted DNA
5.4. Precipitating Nucleic Acids
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
5.18. The Perfect Genomic Library
5.18.1. Lambda (λ) Phage as a Vector
5.19. Complementary DNA (cDNA) Cloning
5.20. Enzymes Used in Molecular Biology Experiments
5.21. Isolating a Specific Gene From a Library
5.22. Labeling Probes by a Variety of Methods
5.23. Baculovirus Vectors for Expressing Foreign Polypeptides in Insect Cells
5.24. Microarray Analysis
Chapter 6: DNA Sequencing and the Evolution of the ``-Omics´´
6.3. The Dideoxy or Chain-Terminating Method
6.4. Shotgun Strategies for Genomes
6.5. Automated Sanger Sequencers
6.6. Analyzing DNA Sequence Data
6.8. A Brief History of the Drosophila Genome Project
6.8.1. The Original Drosophila Genome Project
6.8.2. Actual Drosophila Genome Project
6.8.3. Drosophila Genome Analysis
6.8.4. Surprises in the Drosophila Genome
6.9. Next-Generation Sequencing Methods and Beyond
6.9.1. Second-Generation Methods
6.9.2. Third-Generation Sequencing
6.9.3. A DNA Sequencer in Every Pocket?
6.11. Genome Analyses of Other Arthropods
6.11.1. What Do You Need to Do to Sequence Your Favorite Insects Genome?
6.12. TEs as Agents of Genome Evolution
6.15. Proteomics: Another ``-Omic´´
6.16. Functional Genomics
6.17. Structural Genomics—Another New Horizon?
6.18. Comparative Genomics
6.19. The Post-Genomic Era: Systems Genetics
6.20. The Earth Bio-Genome Project (EBP)
Chapter 7: DNA Amplification by the Polymerase Chain Reaction: Providing a Revolutionary Method for All Biologists
7.3. The Basic Polymerase Chain Reaction (PCR)
7.3.1. The First Few Cycles Are Critical
7.3.3. Standard PCR Protocols
7.3.5. Other Thermostable DNA Polymerases
7.3.6. Primers Are Primary
7.3.7. Storing Insects for the PCR
7.3.8. Preparing DNA Samples
7.3.10. Specificity of the PCR
7.3.11. Detecting Primer Artifacts
7.3.12. How Many Cycles Does a PCR Need?
7.3.13. Reducing the Evils of Contamination
7.4. Some Modifications of the PCR
7.4.1. AFLP for DNA Fingerprinting
7.4.5. Degenerate Primers
7.4.9. Long PCR or High-Fidelity PCR
7.4.13. Quantitative PCR (qPCR)
7.4.16. Reverse-Transcription PCR
7.5. Some Research Applications
7.5.1. Amplifying Ancient DNA
7.5.2. Amplifying Old DNA
7.5.3. Detecting Pathogens in Vector Arthropods
7.5.4. Detecting Pesticide Resistance
7.5.6. Evaluate Efficacy of Disease Control
7.5.7. Evolutionary Analyses
7.6. Multiple Displacement Amplification (MDA): Another Method to Amplify DNA
Chapter 8: Transposable-Element Vectors and Other Methods to Genetically Modify Drosophila and Other Insects
8.3. P Elements and Hybrid Dysgenesis
8.4. P-Element Structure Varies
8.5. Transposition Method of P Elements
8.6. Origin of P Elements in D. melanogaster
8.7. P Vectors and Germ-Line Transformation
8.7.2. Characterizing Transformants
8.8. Using P-Element Vectors
8.9. Transformation of Other Insects With P Vectors
8.10. Evolution of Resistance to Transposable Elements
8.11. Using P to Drive Genes Into Populations
8.12. Other TEs Can Transform D. melanogaster
8.13. Improved Transformation Tools for Drosophila
8.14. TE Vectors to Transform Insects Other Than Drosophila
8.15. Cross Mobilization of TE Vectors
8.16. Conversion of Inactive TE Vectors to Activity
8.17. Suppression of Transgene Expression
8.18. Other Transformation Methods
8.18.1. RNAi for Drosophila
8.18.2. Zinc-Finger Nucleases (ZFNs)
8.18.3. Transcription Activator-Like Effector Nucleases (TALENs)
8.18.4. Meganucleases (or Homing Endonucleases)
Chapter 9: CRISPR-Cas Genome Editing: Another Revolution in Molecular Biology
9.2.2. Origin of CRISPR Systems
9.2.3. Diversity of CRISPR Types
9.2.4. How CRISPR-Cas Works
9.3.1. Choosing Guide RNAs
9.3.2. How to Insert Components Into Preblastoderm Embryos
9.3.3. How to Identify Modified Insects
9.3.4. Identifying Specific Genes
9.3.5. Gene Drives to Control Insects
9.5. Regulatory and Ethical Issues
9.6. Other Systems in the Future?
Part III: Applications in Entomology
Chapter 10: Sex Determination in Insects
10.3. Costs and Benefits of Sexual Reproduction
10.3.1. Sexual Reproduction Has Costs
10.3.2. Advantages of Sex Must Be Large
10.4. Sex Determination Involves Soma and Germ-Line Tissues
10.5. Sex Determination in D. melanogaster
10.5.1. Dosage Compensation of X Chromosomes
10.5.2. Somatic-Sex Determination
10.5.3. Germ-Line Determination
10.6. Are Sex-Determination Mechanisms Diverse?
10.6.1. Intraspecific Variability
10.6.2. Environmental Effects
10.6.3. Postzygotic Sex Determination
10.8. Meiotic Drive Can Distort Sex Ratios
10.8.1. Segregation Distorter (SD)
10.8.2. Distorter in Mosquitos
10.8.3. Female-Biased Sex Ratios in Stalk-Eyed Flies
10.8.4. Meiotic Drive as a Pest-Management Tool?
10.10. Medea in Tribolium
10.11. Cytoplasmic Agents Distort Normal Sex Ratios
10.12. Paternal Sex-Ratio Chromosomes and Cytoplasmic Incompatibility in Nasonia
10.13. Male Killing in Coccinellidae
10.14. Sex and the Sorted Insects
10.14.2. Genetic Improvement of Parasitoids
Chapter 11: Molecular Genetics of Insect Behavior
11.3. The Insect Nervous System
11.4. Traditional Genetic Analyses of Behavior
11.4.1. Crossing Experiments
11.4.2. Selection Experiments
11.4.3. Some Polygenically Determined Behaviors
11.5. Molecular-Genetic Analyses of Insect Behavior
11.5.1. The Photoperiodic Clock
11.5.2. Learning in Drosophila
11.5.3. Functional Genomics of Odor Behavior in Drosophila
11.5.4. Behavior of Apis mellifera
11.5.5. Pheromones in Insects
11.5.6. Neurobiochemistry of Drosophila
11.5.7. Divergent Functions of Est-6 and Est-5 in Two Drosophila Species: A Cautionary Tale of Homologs
11.5.8. Courtship Behavior in Drosophila
11.5.9. Speciation Genes in Drosophila and Other Insects
11.5.10. Personality in Insects: Tribolium confusum, Apis mellifera, Acyrthosiphon pisum, and Pyrrhocoris apterus
11.5.11. Transition From Blood Feeding to Obligate Nonbiting in a Mosquito
11.6. Symbionts and Insect Behavior
11.7. Human Neurodegenerative Diseases and Addictions in Drosophila
11.8. High-Throughput Ethomics
11.9. Systems Genetics of Complex Traits in Drosophila
11.10. Social Behavior in Bees and Ants
Chapter 12: Molecular Systematics and the Evolution of Arthropods
12.3. Controversies in Molecular Systematics and Evolution
12.3.1. Molecular Versus Morphological Traits
12.3.2. The Molecular Clock
12.3.3. The Neutral (or Nearly Neutral) Theory of Evolution
12.3.4. Homology and Similarity
12.4. Molecular Methods for Molecular Systematics and Evolution
12.4.2. Targets of DNA Analysis
12.4.3. High-Throughput Genomic Data
12.4.3.1. RadSeq Analyses
12.4.3.2. Ultraconserved Elements (UCEs)
12.4.3.3. Anchored Hybrid Enrichment (AHE)
12.5. Steps in Phylogenetic Analysis of DNA Sequence Data
12.5.1. Gene Trees or Species Trees
12.5.2. Rooted or Unrooted Trees
12.5.4. Project Goals and Appropriate DNA Sequences
12.5.5. Sequence Comparisons With BLAST
12.5.6. Aligning Sequences
12.5.7. Constructing Phylogenies
12.6. The Universal Tree of Life
12.6.2. Origin of Eukaryota
12.7. The Fossil Record of Arthropods
12.8. Molecular Analyses of Arthropod Phylogeny
12.8.1. Evolution of the Ecdysozoa
12.8.2. Relationships Among the Arthropoda
12.8.3. The Phylogeny of the Holometabola
12.8.4. Congruence Between Morphology- and Molecular-Based Trees
12.8.5. Genomes and Arthropod Phylogenies
12.9. Molecular Evolution and Speciation
12.9.2. How Many Genes Are Involved in Speciation?
12.9.3. Detecting Cryptic Species
Chapter 13: Insect Population Ecology and Molecular Genetics
13.3. What is Molecular Ecology?
13.4. Collecting Arthropods for Analysis
13.5. Molecular Ecological Methods
13.5.1. Allele-Specific PCR
13.5.2. Allozymes (Protein Electrophoresis)
13.5.3. Amplified Fragment Length Polymorphisms (AFLP-PCR)
13.5.4. Double-Strand Conformation Polymorphism (DSCP)
13.5.10.2. Next-Generation Sequencing
13.6. Analyses of Molecular Data
13.7. Case Studies in Molecular Ecology and Population Biology
13.7.1. Genetic Variability in the Fall Armyworm: ``Incipient´´ Species or Multiple Species?
13.7.2. Analyses of Natural Enemies
13.7.2.1. Analyses of Adult Parasitoid Wasps To Reveal Larval Hosts (MAPL)
13.7.2.2. Analyses of the Establishment of a Parasitoid Released in a Classical Biological Control Program
13.7.2.3. Gut Analyses of Predatory Insects to Reveal Prey Species
13.7.3. Population Isolation and Introgression in Periodical Cicadas
13.7.4. Eradicating Medflies in California?
13.7.4.1. The Controversy
13.7.4.2. Species-Specific Diagnostics
13.7.4.3. Geographic Origin of Medfly Populations
13.7.4.4. Is the Medfly Established in California?
13.7.4.6. Some Lessons Learned
13.7.5. Plant Responses to Insect Herbivory
13.7.6. Origins of Insect Populations
13.7.6.1. Emerald Ash Borer
13.7.6.2. Origins of Domesticated Populations of Aedes aegypti
13.7.6.3. Bumblebees From Greenhouses Invade Wild Conspecific Populations
13.7.6.4. Populations of Aedes taeniorhynchus in the Galapagos Islands: Rapid Evolution of an Invasive Species
13.7.6.5. Industrial Melanism in Peppered Moths
13.8. Applied Pest Management
13.8.1. Monitoring Biotypes, Species, and Cryptic Species
13.8.1.1. The Evolution of the Bed Bug to Pest Status
13.8.1.2. Adaptation to an Agricultural Environment by the Cabbage White Butterfly, Pieris rapae
13.8.2. Monitoring Vectors of Disease
13.8.3. Pesticide Resistances and Pest Management
13.8.4. Monitoring Pest-Population Biology
13.8.5. The ``So What?´´ Test
Chapter 14: Genetic Modification of Pest and Beneficial Insects for Pest Management Programs
14.3. Why Genetically Modify Insects?
14.3.1. Beneficial Insects
14.4. Why Use Molecular-Genetic Methods?
14.5. What Genetic Modification Methods are Available?
14.5.1. Transposable-Element (TE) Vectors and Transgenesis
14.5.2. Paratransgenesis (Genetic Modification of Symbionts)
14.5.4. Transfer of Wolbachia From Another Arthropod
14.5.5. Site-Specific Modifications: ZFNs, TALENs, and CRISPR Systems
14.5.6. RNAi to Control Pests
14.5.6.1. RNAi in Crop Plants
14.6. Methods to Deliver Exogenous Nucleic Acids Into Arthropod Tissues
14.7. What Genes to Target?
14.8. Why Are Regulatory Signals Important?
14.9. How Are Modified Arthropods Identified?
14.10. How to Deploy Genetically Modified Pest and Beneficial Arthropods
14.11. Potential Risks Associated With Releases of Genetically Modified Arthropods
14.11.1. Could Gene Silencing/Loss Reduce Program Effectiveness?
14.11.3. General Risk Issues
14.11.4. Horizontal Transfer (HT)
14.12. Permanent Releases of Genetically Modified Arthropods Into the Environment
14.12.1. Models to Predict
14.13. Regulatory Issues: Releases of Genetically Modified Arthropods
Insect Molecular Genetics
：An Introduction to Principles and Applications
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