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 β-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