Molecular Biotechnology: Principles and Applications of Recombinant DNA

ISBN-13: 9781683673644 / Angielski / Twarda / 2022 / 896 str.

Bernard R. Glick; Cheryl L. Patten

Spis treści

1.The Development of Molecular Biotechnology 1Emergence of Molecular Biotechnology 1Recombinant DNA Technology 3Commercialization of Molecular Biotechnology 6Concerns and Consequences 8Summary 10References 10Review Questions 112.Fundamental Technologies 13Molecular Cloning 13Preparation of DNA for Cloning 13Insertion of Target DNA into a Plasmid Vector 18Transformation and Selection of Cloned DNA in a Bacterial Host 21Cloning Eukaryotic Genes 26Recombinational Cloning 30Genomic Libraries 32Genome Engineering Using CRISPR Technology 36Polymerase Chain Reaction 39Amplification of DNA by PCR 39Cloning PCR Products 42Quantitative PCR 44Chemical Synthesis of Genes 46Assembling Oligonucleotides into Genes 46Assembling PCR Products into Genes 46DNA Sequencing Technologies 48Dideoxynucleotide Sequencing 50Sequencing Using Reversible Chain Terminators 53Single-Molecule Real-Time Sequencing 55Nanopore Sequencing 56Sequencing Whole Genomes 56Preparation of Genomic DNA Sequencing Libraries 57High-Throughput Next-Generation Sequencing 59Genome Sequence Assembly 60Sequencing Metagenomes 61Genomics 62Transcriptomics 65Proteomics 70Metabolomics 84Summary 86References 87Review Questions 893.Production of Recombinant Proteins 91Protein Production in Prokaryotic Hosts 91Regulating Transcription 92Increasing Translation Efficiency 96Increasing Protein Stability 100Increasing Protein Secretion 105Facilitating Protein Purification 111Integrating DNA into the Host Chromosome 114Heterologous Protein Production in Eukaryotic Cells 119Posttranslational Modification of Eukaryotic Proteins 120General Features of Eukaryotic Expression Systems 123Yeast Expression Systems 123Baculovirus-Insect Cell Expression Systems 137Mammalian Cell Expression Systems 145Protein Engineering 156Directed Mutagenesis 156Random Mutagenesis 161Examples of Protein Engineering 164Summary 173References 174Review Questions 1764.Molecular Diagnostics 179Immunological Approaches To Detect Protein Biomarkers 180Antibodies 180Agglutination 185Enzyme-Linked Immunosorbent Assays 186Protein Arrays To Detect Polygenic Diseases 194Immunoassays for Protein Conformation-Specific Disorders 197DNA-Based Diagnostic Approaches 199Hybridization Probes 199PCR-Based Detection Methods 207CRISPR-Cas-Based Diagnostic Assays 218DNA Microarrays 219Whole-Genome Sequencing To Assess Genetic Disease Risk 225Detecting RNA Signatures of Disease 226Detection of Disease-Associated Changes in Gene Expression 227Detection of RNA Signatures of Antibiotic Resistance in Bacteria 228Detection of miRNA Signatures of Disease 230Biofluorescent and Bioluminescent Systems 233Fluorescent Proteins 233Luciferase 234Microbial Biosensors 235Summary 238References 239Review Questions 2415.Protein Therapeutics 243Pharmaceuticals 244Human Interferons 244Human Growth Hormone 248Tumor Necrosis Factor Alpha 251Extending Protein Half-Life 252Enzymes 253DNase I 253Alginate Lyase 254Phenylalanine Ammonia Lyase 258alpha1 -Antitrypsin 259Glycosidases 261Masking Nonhuman Epitopes 263Toxin-Intein Fusions 264Targeting Mitochondria 265Bacteria and Therapeutics 267Interleukin-10 270Leptin 272An HIV Inhibitor 274Insulin 276Parkinson's Disease 279Cancer and Bacteria 279Recombinant Antibodies 280Hybrid Human-Mouse Monoclonal Antibodies 284Human Monoclonal Antibodies 287Antibody Fragments 289Combinatorial Libraries of Antibody Fragments 294A Combinatorial Library of Full-Length Antibodies 297Shuffling CDR Sequences 298Dual-Variable-Domain Antibodies 298Bispecific Antibodies against Hemophilia 300Anti-HIV Antibodies 300Anticancer Antibodies 302Antibodies against Various Diseases 309Antiobesity Antibodies 313Enhanced Antibody Half-Life 315Affibody Molecules 315Summary 318References 318Review Questions 3226. Nucleic Acids as Therapeutic Agents 325Targeting Specific mRNA and DNA Sequences 327Antisense RNA 327Aptamers 331Ribozymes and DNAzymes 338Interfering RNA 341Zinc Finger Nucleases 348CRISPR-Cas System 349Nanozymes 351Nanoparticles 352Engineering Bacteriophages 352Viral Delivery Systems 357Nonviral Delivery Systems 365Direct Injection 365Lipids 367Bacteria 369Dendrimers 372Antibodies 373Aptamers 373Transposons 374Gene Therapy 376Mitochondrial Diseases 378Prodrug Activation Therapy 378Promoterless Gene Targeting 379Summary 382References 382Review Questions 3867. Vaccines 387Vaccination 387Current and Future Vaccines 389Subunit and Peptide Vaccines 392Herpes Simplex Virus 393Bovine Herpes Virus-1 394Cholera 396Influenza 396SARS 397COVID-19 399Staphylococcus aureus 401Human Papillomavirus 402Foot-and-Mouth Virus 404Streptococcus 405Peptides 407Malaria 408Delivery 411Genetic Immunization: DNA Vaccines 414Delivery 414Cancer 422Zika Virus 422Dental Caries 423Engineered Attenuated Vaccines 424Herpes Simplex Virus 425Cholera 426Salmonella Species 428Leishmania Species 430Vector Vaccines 430Vaccines Directed against Viruses 430Vaccines Directed against Bacteria 441Bacteria as Antigen Delivery Systems 444Monoclonal Antibody Passive Immunity 449Influenza Virus 450Summary 452References 452Review Questions 4568. Industrial and Environmental Uses of Recombinant Microorganisms 459Restriction Endonucleases 459Small Biological Molecules 461l-Ascorbic Acid 463Indigo 467Amino Acids 468Lycopene 473Antibiotics 474Biopolymers 487Solvent Tolerance 493Systems Metabolic Engineering To Optimize Product Yield 494Microbial Degradation of Xenobiotics 496Genetic Engineering of Biodegradative Pathways 497Plastics 507Utilization of Starch and Sugars 508Commercial Production of Fructose and Alcohol 508Increasing Alcohol Production 510Improving Fructose Production 517Utilization of Cellulose and Hemicellulose 518Lignocellulosics 519Cellulase Genes 522Direct Conversion of Biomass to Ethanol 530Alcohol Production by Zymomonas mobilis 531Lipids from Cyanobacteria 534Hydrogen Production 535Summary 538References 539Review Questions 5429. Large-Scale Production of Proteins and Nucleic Acids from Recombinant Microorganisms 545Principles of Microbial Growth 547Batch Fermentation 548Fed-Batch Fermentation 549Continuous Fermentation 550Maximizing the Efficiency of the Fermentation Process 551High-Density Cell Cultures 552Increasing Plasmid Stability 555Quiescent E. coli Cells 555Protein Secretion 558Reducing Acetate 558Improving Antibody Production in E. coli 561Bioreactors 561Typical Large-Scale Fermentation Systems 565Two-Stage Fermentation in Tandem Airlift Reactors 566Two-Stage Fermentation in a Single Stirred-Tank Reactor 568Batch versus Fed-Batch Fermentation 569Harvesting Microbial Cells 574Disrupting Microbial Cells 576Downstream Processing 578Inclusion Bodies 579Utilizing an Immobilized Enzyme 582Magnetic Separation of Proteins 582Large-Scale Production of DNA and RNA 583Plasmid DNA 583mRNA 586Summary 587References 587Review Questions 59010. Genetic Engineering of Plants: Methodology 591Plant Transformation with the Ti Plasmid of A. tumefaciens 595Ti Plasmid-Derived Vector Systems 597Increasing Transformation Efficiency 601Microprojectile Bombardment 603Chloroplast Engineering 604Very-High-Level Protein Expression 607Use of Reporter Genes in Transformed Plant Cells 610Manipulation of Gene Expression in Plants 611Transient Gene Expression 611Plant Promoters 616Manipulation of Genes in Plants 617Facilitating Protein Purification 621Protein Glycosylation 623Gene Stacking 624CRISPR-Based Directed Evolution 625Polycistronic Gene Expression 626Production of Marker-Free Transgenic Plants 626Removing Marker Genes from Nuclear DNA 627Removing Marker Genes from Chloroplast DNA 632Summary 633References 634Review Questions 63611. Transgenic Plants 637Insect Resistance 637Bacillus thuringiensis Insecticidal Toxin 637Increasing Expression of the B. thuringiensis Protoxin 642Other Strategies for Protecting Plants against Insects 645Preventing the Development of B. thuringiensis-Resistant Insects 652Targeting Aphids 657Virus Resistance 658Viral Coat Protein-Mediated Protection 658Protection by Expression of Other Genes 663Herbicide Resistance 668Glyphosate 669Dicamba 672Other Herbicides 673Fungus and Bacterium Resistance 674Transgenic Plants 675RNAi and CRISPR/Cas 681Salt and Drought Stress 682Increasing Trehalose Production 683Sequestering Sodium Ions 684Delaying Drought-Induced Senescence 685Phytoremediation 686Fruits and Flowers 688Flavr Savr Tomato 688Lowering Ethylene Levels 688CRISPR Mutants 690Modification of Plant Nutritional Content 690Amino Acids 690Lipids 692Vitamins 695Iron 698Gluten 700Modification of Food Plant Taste and Appearance 701Preventing Discoloration 701Starch 703Plants as Bioreactors 706Antibodies 706Pharmaceuticals and Vaccines 709Poly(3-Hydroxybutyric Acid) 710Edible Vaccines 711Edible Cholera Vaccines 712Edible E. coli Vaccines 714Plant Yield 716Increasing Grain Yield 716Increasing Harvest Index 716Decreasing Lignin Content 717Decreasing Pectin Content 720Increasing Oxygen Content 722Summary 723References 724Review Questions 72912. Transgenic Animals 731Transgenic Animal Methodologies 733DNA Microinjection Method 733Retroviral Vector Method 736Engineered Embryonic Stem Cell Method 737Somatic Cell Nuclear Transfer for Transgenic Livestock 743Genome Editing with the CRISPR-Cas System 744Conditional Gene Modification with the Cre-loxP Recombination System 747Control of Transgene Expression with the Tetracycline-Inducible System 749Gene Knockdown by RNA Interference 754Transgenic Animal Models of Human Diseases 756Mouse Models of Alzheimer's Disease 756Mouse Model of Duchenne Muscular Dystrophy 759Rabbit Models of Cardiovascular Disease 761Zebrafish Melanoma Model 763Nonhuman Primate Models of NeurodevelopmentalDisorders 766Animal Bioreactors for Production of Recombinant Therapeutic Proteins 767Production of Recombinant Antithrombin in Goat Milk 768Production of a Human Protease Inhibitor in Rabbits 770Production of Therapeutic Proteins in Chicken Eggs 771Production of Donor Organs in Pigs 773Enhancing Production Traits of Food Animals 774Disease-Resistant Livestock 774Improving Milk Quality 781Increasing Muscle Mass in Cattle 782Enhancing Growth of Salmon 786Gene Drives To Eradicate Vector-Transmitted Diseases 787Malaria Vector Population Suppression 789Dengue Fever Virus-Resistant Mosquitoes 791Reversal Drives 792Summary 795References 796Review Questions 79713. Molecular Biotechnology and Society 799Development of Guidelines for Recombinant DNA Research 800Deliberate Release of Genetically Modified Microorganisms 802Environmental Concerns 802Regulations 803Regulation of Genetically Modified Foods 804Food Ingredients Produced by Genetically Engineered Microorganisms 804Genetically Modified Crops 807Genetically Engineered Livestock 810Societal Concerns about Genetically Modified Foods 812Alteration of Nutritional Content of Food 812Potential for Introducing Toxins or Allergens into Food 816Potential for Transferring Transgenes from Food to Humans or Intestinal Microorganisms 819Controversy about the Labeling of Genetically Modified Foods 820Impact of Genetically Engineered Crops on Biodiversity 822Who Benefits from the Production of Genetically Modified Foods? 824Environmental Benefits of Genetically Modified Crops 825How Do Views about Genetically Engineered Organisms Impact Trade? 827Regulation and Safety of Medical Products of Biotechnology 827New Biological Drugs 828Genetic and Genomic Testing 832Economic Issues 835Patenting Biotechnology 837Patenting 838Patenting in Different Countries 839Patenting Nucleic Acid Sequences 841Patenting Living Organisms 842Patenting and Fundamental Research 844Summary 845References 846Review Questions 848Amino Acids of Proteins and Their Designations 851Index 853

O autorze

About the AuthorsBernard R. Glick, PhD, is a distinguished professor emeritus at the University of Waterloo, Ontario, Canada, where he was the chair of biology from 2002 to 2008. He has authored more than 400 publications that have garnered over 54,000 citations.Cheryl L. Patten, PhD, is a professor of microbiology in the Biology Department at the University of New Brunswick, Fredericton, Canada. She teaches courses in introductory biology, microbiology, and biotechnology.