Chapter 1. Basics of Biotechnology

• Advent of the Biotechnology Revolution
• Chemical Structure of Nucleic Acids
• Packaging of Nucleic Acids
• Bacteria as the Workhorses of Biotechnology
• Escherichia coli Is the Model Bacterium
• Many Bacteria Contain Plasmids
• Other Bacteria in Biotechnology
• Basic Genetics of Eukaryotic Cells
• Yeast and Filamentous Fungi in Biotechnology
• Yeast Mating Types and Cell Cycle
• Multicellular Organisms as Research Models
• Animal Cell Culture in Vitro
• Arabidopsis thaliana, a Model Flowering Plant
• Viruses Used in Genetics Research
• Subviral Infectious Agents and Other Gene Creatures
• Summary

Chapter 2. DNA, RNA, and Protein

• The Central Dogma of Molecular Biology
• Transcription Expresses Genes
• Making RNA
• Transcription Stop Signals
• The Number of Genes on an mRNA Varies
• Eukaryotic Transcription is More Complex
• Regulation of Transcription in Prokaryotes
• Regulation of Transcription in Eukaryotes
• Eukaryotic mRNA is Processed Before Making Protein
• Translating the Genetic Code into Proteins
• Differences between Prokaryotic and Eukaryotic Translation
• Mitochondria and Chloroplasts Synthesize Their Own Proteins
• Summary

Chapter 3. Recombinant DNA Technology

• DNA Isolation and Purification
• Electrophoresis Separates DNA Fragments by Size
• Restriction Enzymes Cut DNA; Ligase Joins DNA
• Methods of Detection for Nucleic Acids
• Complementary Strands Melt Apart and Reanneal
• Hybridization of DNA or RNA in Southern and Northern Blots
• Fluorescence in Situ Hybridization (FISH)
• General Properties of Cloning Vectors
• Specific Types of Cloning Vectors
• Getting Cloned Genes into Bacteria by Transformation
• Constructing a Library of Genes
• Screening the Library of Genes by Hybridization
• Eukaryotic Expression Libraries
• Features of Expression Vectors
• Recombineering Increases the Speed of Gene Cloning
• Gateway^® Cloning Vectors
• Summary

Chapter 4. DNA Synthesis In Vivo and In Vitro

• Introduction
• Replication of DNA
• Comparing Replication in Gene Creatures, Prokaryotes, and Eukaryotes
• In Vitro DNA Synthesis
• Chemical Synthesis of DNA
• Chemical Synthesis of Complete Genes
• Polymerase Chain Reaction Uses in Vitro Synthesis to Amplify Small Amounts of DNA
• Modifications of Basic PCR
• Reverse Transcriptase PCR
• PCR in Genetic Engineering
• PCR of DNA can Determine the Sequence of Bases
• Next-Generation Sequencing Technologies
• Summary

Chapter 5. RNA-Based Technologies

• Noncoding RNA Plays Many Roles
• RNA Coordinates Genomic Integrity in Eukaryotes
• RNA Protects Genomes from Invading Viruses
• RNA Modulates Transcription
• Noncoding RNAs Take Part in RNA Processing
• Riboswitches are Controlled by Effector Molecules
• RNA Catalyzes Enzyme Reactions
• Summary

Chapter 6. Immune Technology

• Introduction
• Antibodies, Antigens, and Epitopes
• The Great Diversity of Antibodies
• Structure and Function of Immunoglobulins
• Monoclonal Antibodies for Clinical Use
• Humanization of Monoclonal Antibodies
• Humanized Antibodies in Clinical Applications
• Antibody Engineering
• Diabodies and Bispecific Antibody Constructs
• ELISA Assay
• The ELISA as a Diagnostic Tool
• Visualizing Cell Components using Antibodies
• Fluorescence-Activated Cell Sorting
• Immune Memory and Vaccination
• Creating a Vaccine
• Making Vector Vaccines using Homologous Recombination
• Reverse Vaccinology
• Identifying New Antigens for Vaccines
• DNA Vaccines Bypass the need to Purify Antigens
• Edible Vaccines
• Summary

Chapter 7. Nanobiotechnology

• Introduction
• Visualization at the Nanoscale
• Scanning Tunneling Microscopy
• Atomic Force Microscopy
• Weighing Single Bacteria and Virus Particles
• Nanoparticles and Their Uses
• Nanoparticles for Labeling
• Quantum Size Effect and Nanocrystal Colors
• Nanoparticles for Delivery of Drugs, DNA, or RNA
• Nanoparticles in Cancer Therapy
• Assembly of Nanocrystals by Microorganisms
• Nanotubes
• Antibacterial Nanocarpets
• Detection of Viruses by Nanowires
• Ion Channel Nanosensors
• Nanoengineering of DNA
• DNA Origami
• DNA Mechanical Nanodevices
• Controlled Denaturation of DNA by Gold Nanoparticles
• Controlled Change of Protein Shape by DNA
• Biomolecular Motors
• Summary

Chapter 8. Genomics and Gene Expression

• Introduction
• Genetic Mapping Techniques
• Gaps Remain in the Human Genome
• Survey of the Human Genome
• Noncoding Components of the Human Genome
• Bioinformatics and Computer Analysis
• Medicine and Genomics
• DNA Accumulates Mutations over Time
• Genetic Evolution
• From Pharmacology to Pharmacogenetics
• Gene Expression and Microarrays
• Making DNA Microarrays
• Hybridization ON DNA Microarrays
• Monitoring Gene Expression Using Whole-Genome Tiling Arrays
• Monitoring Gene Expression by RNA-Seq
• Monitoring Gene Expression of Single Genes
• Epigenetics and Epigenomics
• Epigenomics in Higher Organisms
• Summary

Chapter 9. Proteomics

• Introduction
• Gel Electrophoresis of Proteins
• Western Blotting of Proteins
• High-Pressure Liquid Chromatography Separates Protein Mixtures
• Digestion of Proteins by Proteases
• Mass Spectrometry for Protein Identification
• Preparing Proteins for Mass Spectroscopy
• Protein Quantification Using Mass Spectrometry
• Protein Tagging Systems
• Phage Display Library Screening
• Protein Interactions: The Yeast Two-Hybrid System
• Protein Interactions by Co-immunoprecipitation
• Protein Arrays
• Metabolomics
• Summary

Chapter 10. Recombinant Proteins

• Proteins and Recombinant DNA Technology
• Expression of Eukaryotic Proteins in Bacteria
• Insulin and Diabetes
• Cloning and Genetic Engineering of Insulin
• Translation Expression Vectors
• Codon Usage Effects
• Avoiding Toxic Effects of Protein Overproduction
• Inclusion Bodies and Protein Refolding
• Increasing Protein Stability
• Improving Protein Secretion
• Protein Fusion Expression Vectors
• Protein Glycosylation
• Expression of Proteins by Eukaryotic Cells
• Expression of Proteins by Yeast
• Expression of Proteins by Insect Cells
• Expression of Proteins by Mammalian Cells
• Expression of Multiple Subunits in Mammalian Cells
• Comparing Expression Systems
• Summary

Chapter 11. Protein Engineering

• Introduction
• Engineering Disulfide Bonds
• Improving Stability In Other Ways
• Changing Binding Site Specificity
• Structural Scaffolds
• Directed Evolution
• Recombining Domains
• DNA Shuffling
• Combinatorial Protein Libraries
• Creation of De Novo Proteins
• Expanding the Genetic Code
• Roles of Non-Natural Amino Acids
• Biomaterials Design Relies on Protein Engineering
• Engineered Binding Proteins
• Summary

Chapter 12. Environmental Biotechnology

• Introduction
• Identifying New Genes with Metagenomics
• Culture Enrichment for Environmental Samples
• Sequence-Dependent Techniques for Metagenomics
• Function- or Activity-Based Evaluation of The Environment
• Ecology and Metagenomics
• Natural Attenuation of Pollutants
• Biofuels and Bioenergy
• Microbial Fuel Cells
• Summary

Chapter 13. Synthetic Biology

• Introduction
• Ethanol, Elephants, and Pathway Engineering
• Degradation of Starch
• Degradation of Cellulose
• Second-Generation Biofuels
• Biodiesel
• Ice-Forming Bacteria and Frost
• Biorefining of Fossil Fuels
• Biosynthesis of ß-Lactam Antibiotics
• Biosynthetic Plastics are Also Biodegradable
• The Integrated Circuits Approach
• Synthetic Genetic Materials: xDNA And XNA
• Designer Bacteria
• Summary

Chapter 14. From Cell Phones to Cyborgs

• Introduction
• Cell Phones
• Robotics
• Radio-Controlled Genes
• Insect Cyborgs
• Soft Robotics
• Summary

Chapter 15. Transgenic Plants and Plant Biotechnology

• Introduction
• History of Plant Breeding
• Plant Tissue Culture
• Genetic Engineering of Plants
• Biotechnology Improves Crops
• Resistance: Nature Responds to Transgenic Plants
• Functional Genomics in Plants
• Summary

Chapter 16. Transgenic Animals

• New and Improved Animals
• Creating Transgenic Animals
• Larger Mice Illustrate Transgenic Technology
• Recombinant Protein Production Using Transgenic Livestock
• Knockout Mice for Medical Research
• Alternative Ways to Make Transgenic Animals
• Location Effects on Expression of the Transgene
• Deliberate Control of Transgene Expression
• Gene Control by Site-Specific Recombination
• Transgenic Insects
• Practical Transgenic Animals
• Applications of RNA Technology in Transgenics
• Natural Transgenics and DNA Ingestion
• Summary

Chapter 17. Inherited Defects and Gene Therapy

• Introduction
• Hereditary Defects in Higher Organisms
• Hereditary Defects Due to Multiple Genes
• Defects Due to Haploinsufficiency
• Dominant Mutations may be Positive or Negative
• Deleterious Tandem Repeats and Dynamic Mutations
• Defects in Imprinting and Methylation
• Mitochondrial Defects
• Identification of Defective Genes
• Genetic Screening and Counseling
• General Principles of Gene Therapy
• Adenovirus Vectors in Gene Therapy
• Cystic Fibrosis
• Cystic Fibrosis Gene Therapy
• Retrovirus Gene Therapy
• Retrovirus Gene Therapy for Scid
• Adeno-Associated Virus
• Nonviral Delivery in Gene Therapy
• Liposomes and Lipofection in Gene Therapy
• Aggressive Gene Therapy for Cancer
• Using RNA in Therapy
• Antisense RNA and Other Oligonucleotides
• Aptamers—Blocking Proteins with DNA or RNA
• Ribozymes in Gene Therapy
• RNA Interference in Gene Therapy
• Gene Editing with Nucleases
• Genome Editing with Engineered Nucleases
• Genome Editing with CRISPR Nucleases
• Summary

Chapter 18. Cloning and Stem Cells

• Introduction
• What is a Stem Cell?
• Identifying Adult Stem Cells
• The Key Features of a Stem Cell Niche
• Hematopoietic Stem Cells in the Bone Marrow
• Intestinal Epithelial Stem Cells
• Induced Pluripotent Stem Cells
• Stem Cell Therapy
• Somatic Cell Nuclear Transfer
• Dolly the Cloned Sheep
• Practical Reasons for Cloning Animals
• Improving Livestock by Pathway Engineering
• Imprinting and Developmental Problems in Cloned Animals
• Summary

Chapter 19. Cancer

• Cancer is Genetic in Origin
• Environmental Factors and Cancer
• Normal Cell Division: The Cell Cycle
• Cellular Communication
• Receptors and Signal Transmission
• Cell Division Responds to External Signals
• Genes that Affect Cancer
• Oncogenes and Proto-Oncogenes
• Detection of Oncogenes by Transformation
• Types of Mutations that Generate Oncogenes
• The RAS Oncogene—Hyperactive Protein
• The MYC Oncogene—Overproduction of Protein
• Tumor-Suppressor Genes or Anti-Oncogenes
• The p16, p21, and p53 Anti-Oncogenes
• Formation of a Tumor
• Inherited Susceptibility to Cancer
• Cancer-Causing Viruses
• Engineered Cancer-Killing Viruses
• Cancer Genomics
• Cancer Epigenomics
• Micro RNA Regulation and Cancer
• Anticancer Agents
• Summary

Chapter 20. Aging and Apoptosis

• Introduction
• Genetic Phenomena Associated with Aging
• Cellular Dysfunction and Aging
• Cellular Senescence
• Programmed Cell Death
• Apoptosis Involves a Proteolytic Cascade
• Mammalian Apoptosis
• Caspases
• Execution Phase of Apoptosis
• Corpse Clearance in Apoptosis
• Control of Apoptotic Pathways in Development
• Necroptosis
• Metabolic Control of Cell Death
• Cancer, Aging, and Programmed Cell Death
• Programmed Cell Death in Bacteria
• Summary

Chapter 21. Viral and Prion Infections

• Viral Infections and Antiviral Agents
• Interferons Coordinate the Antiviral Response
• Antiviral Therapy using RNA Interference
• Influenza is a Negative-Strand Rna Virus
• The AIDS Retrovirus
• Chemokine Receptors Act as Co-Receptors for Hiv
• Treatment of the AIDS Retrovirus
• Infectious Prion Disease
• Detection of Pathogenic Prions
• Approaches to Treating Prion Disease
• Prions in Yeast
• Using Yeast Prions as Models
• Amyloid Proteins in Neurological Diseases
• Summary

Chapter 22. Biological Warfare: Infectious Disease and Bioterrorism

• Introduction
• The Natural History of Biological Warfare
• Microbes Versus Man: The Rise of Antibiotic Resistance
• A Brief History of Human Biological Warfare
• Identifying Suitable Biological Warfare Agents
• A Closer Look at Select Biological Warfare Agents
• Enhancing Biological Warfare Agents with Biotechnology
• Detection of Biological Warfare Agents
• Summary

Chapter 23. Forensic Molecular Biology

• The Genetic Basis of Identity
• Blood, Sweat, and Tears
• Forensic DNA Testing
• DNA Fingerprinting
• Using Repeated Sequences in Fingerprinting
• Probability and DNA Testing
• The Use of DNA Evidence
• DNA is Also Used to Identify Animals
• Tracing Genealogies by Mitochondrial DNA and the Y Chromosome
• Identifying the Remains of the Russian Imperial Family
• Gene Doping and Athletics
• Genomics Drives Advances in Forensics
• Summary

Chapter 24. Bioethics in Biotechnology

• Introduction
• Principles of Bioethics
• Use of the Precautionary Principle
• The Power of Information
• Possible Dangers to Health from Biotechnology
• Genetically Modified Organisms
• Human Enhancement, Cloning, and Engineering
• Ethics Changes over Time
• Summary