Biotechnology Applying the Genetic Revolution

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Biotechnology Applying the Genetic Revolution

Basics of biotechnology


=> Advent of the Biotechnology Revolution
=> Gregor Johann Mendel (1822-1884): Founder of Modern Genetics
=> Chemical Structure of Nucleic Acids
=> Packaging of Nucleic Acids
=> Bacteria as the Workhorses of Biotechnology
=> Escherichia coli Is the Model Bacterium
=> Arabidopsis thaliana , a Model Flowering Plant
=> Viruses Used in Genetics Research
=> Subviral Infectious Agents and Other Gene Creatures

DNA RNA and Protein


=> The Central Dogma of Molecular Biology
=> Transcription Expresses Genes
=> Making the 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

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
=> Subtractive Hybridization

DNA Synthesis in Vivo and in Vitro


=> Introduction of DNA Synthesis in Vivo and in Vitro
=> Replication of DNA
=> Comparing Replication in Gene Creatures, Prokaryotes, and Eukaryotes
=> In Vitro DNA Synthesis
=> Chemical Synthesis of DNA
=> Chemical Synthesis of Complete Genes
=> In Vitro Synthesis of DNA Can Determine the Sequence of Bases
=> Polymerase Chain Reaction Uses In Vitro Synthesis to Amplify Small Amounts of DNA
=> Automated DNA Cycle Sequencing Combines PCR and Sequencing
=> Modifications of Basic PCR
=> Randomly Amplified Polymorphic DNA
=> Reverse Transcriptase PCR
=> PCR in Genetic Engineering

RNA Based Technologies


=> RNA Based Technologies
=> Antisense RNA Modulates mRNA Expression
=> Antisense Oligonucleotides
=> Expression of Antisense RNA Constructs
=> Delivery of Antisense Therapies
=> RNA Interference Uses Antisense Sequences to Inhibit Gene Expression
=> RNAi in Plants and Fungi
=> MicroRNAs Are Antisense RNAs That Modulate Gene Expression
=> Applications of RNAi for Studying Gene Expression
=> RNAi for Studying Mammalian Genes
=> Functional Screening with RNAi Libraries
=> Ribozymes Catalyze Cleavage and Ligation Reactions
=> Small Naturally Occurring Ribozymes
=> Engineering Ribozymes for Medical and Biotechnology Applications
=> RNA SELEX Identifies New Binding Partners for Ribozymes
=> In Vitro Evolution and in Vitro Selection of Ribozymes
=> Synthetic Ribozymes Used in Medicine
=> Allosteric Deoxyribozymes Catalyze Specific Reactions
=> Riboswitches Are Controlled by Effector Molecules
=> Engineering Allosteric Riboswitches and Ribozymes

Immune Technology


=> Antibody Structure and Function
=> Antibodies, Antigens, and Epitopes
=> The Great Diversity of Antibodies
=> Antibody Structure
=> 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

Nanobiotechnology


=> Nanobiotechnology
=> Visualization at the Nanoscale
=> Scanning Tunneling Microscopy
=> Atomic Force Microscopy
=> Virus Detection via AFM
=> 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 Mechanical Nanodevices
=> Controlled Denaturation of DNA by Gold Nanoparticles
=> Controlled Change of Protein Shape by DNA
=> Biomolecular Motors

Genomics and Gene Expression


=> Genomics and Gene Expression
=> Genetic Mapping Techniques
=> Physical Maps Use Sequence Data
=> Radiation Hybrid and Cytogenetic Mapping
=> Sequencing Entire Genomes
=> Race for the Human Genome
=> 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 of Single Genes

Proteomics


=> Proteomics
=> 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
=> Peptide Sequencing Using Mass Spectrometry
=> 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

Recombinant Proteins


=> Proteins and Recombinant DNA Technology
=> Expression of Eukaryotic Proteins in Bacteria
=> Translation Expression Vectors
=> Codon Usage Effects
=> Avoiding Toxic Effects of Protein Overproduction
=> Increasing Protein Stability
=> Improving Protein Secretion
=> Protein Fusion Expression Vectors
=> Expression of Proteins by Eukaryotic Cells
=> Expression of Proteins by Yeast
=> Expression of Proteins by Insect Cells
=> Protein Glycosylation
=> Expression of Proteins by Mammalian Cells
=> Expression of Multiple Subunits in Mammalian Cells
=> Comparing Expression Systems

Protein Engineering


=> Protein Engineering
=> Engineering Disulfide Bonds
=> Improving Stability in Other Ways
=> Changing Binding Site Specificity
=> Structural Scaffolds
=> Directed Evolution
=> Adding New Functional Groups Using Nonnatural Amino Acids
=> Recombining Domains
=> DNA Shuffling
=> Combinatorial Protein Libraries
=> Biomaterials Design Relies on Protein Engineering
=> Engineered Binding Proteins

Environmental Biotechnology


=> Environmental Biotechnology
=> 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

Pathway Engineering


=> Pathway Engineering
=> Ethanol, Elephants, and Pathway Engineering
=> Degradation of Starch
=> Degradation of Cellulose
=> Ice Forming Bacteria and Frost
=> Degradation of Aromatic Ring Compounds
=> Indigo and Related Natural Pigments
=> The Toluene/Xylene Pathway
=> Removal of Halogen, Nitro, and Sulfonate Groups
=> Biorefining of Fossil Fuels
=> Biosynthesis of Medium-Sized Molecules
=> Sterol Synthesis and Modification
=> Biosynthesis of beta Lactam Antibiotics
=> Polyketides and Polyketide Antibiotics
=> Biosynthetic Plastics Are Also Biodegradable

Transgenic Plants and Plant Biotechnology


=> History of Plant Breeding
=> Plant Tissue Culture
=> Genetic Engineering of Plants
=> Getting Genes into Plants Using the Ti Plasmid
=> Particle Bombardment Technology
=> Detection of Inserted DNA
=> Using the Cre/loxP System
=> Plant Breeding and Testing
=> Transgenic Plants with Herbicide Resistance
=> Transgenic Plants with Insect Resistance
=> Trehalose in Transgenic Plants Increase Stress Tolerance
=> Functional Genomics in Plants
=> Food Safety Assessment and Starlink Corn
=> Bt Toxin and Butterflies

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 Approaches to Making Transgenic Animals
=> Location Effects on Expression of the Transgene
=> Combating Location Effects on Transgene Expression
=> Targeting the Transgene to a Specific Location
=> Deliberate Control of Transgene Expression
=> Control by Site-Specific Recombination Using Cre or Flp
=> Transgenic Insects
=> Genetically Modified Mosquitoes
=> Cloning Animals by Nuclear Transplantation
=> Dolly the Cloned Sheep
=> Practical Reasons for Cloning Animals
=> Improving Livestock by Pathway Engineering
=> Problems and Ethics of Nuclear Transplantation
=> Imprinting and Developmental Problems in Cloned Animals
=> Transgenic People, Primates, and Pets
=> Applications of RNA Technology in Transgenics
=> Applications of RNA Interference in Transgenics
=> Natural Transgenics and DNA Ingestion

Inherited Defects


=> Inherited Defects
=> 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, Location, and Cloning of Defective Genes
=> Cystic Fibrosis
=> Muscular Dystrophy
=> Genetic Screening and Counseling

Gene Therapy


=> Gene Therapy or Genetic Engineering?
=> General Principles of Gene Therapy
=> Gene Patching by Oligonucleotide Crossover
=> Aggressive Gene Therapy
=> Adenovirus Vectors in Gene Therapy
=> Cystic Fibrosis Gene Therapy by Adenovirus
=> Adeno Associated Virus
=> Retrovirus Gene Therapy
=> Retrovirus Gene Therapy for SCID
=> Nonviral Delivery in Gene Therapy
=> Liposomes and Lipofection in Gene Therapy
=> Aggressive Gene Therapy for Cancer
=> Antisense RNA and Other Oligonucleotides
=> Aptamers-Blocking Proteins with RNA
=> Ribozymes in Gene Therapy

Molecular Biology of Cancer


=> Cancer Is Genetic in Origin
=> Environmental Factors and Cancer
=> Normal Cell Division: The Cell Cycle
=> 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

Noninfectious Diseases


=> Noninfectious Diseases: Cellular Communication
=> Noninfectious Diseases: Receptors and Signal Transmission
=> Steroids and Other Lipophilic Hormones
=> Cyclic AMP as Second Messenger
=> Nitric Oxide and Cyclic GMP
=> Cyclic Phosphodiesterase and Erectile Dysfunction
=> Insulin and Diabetes
=> The Insulin Receptor
=> Cloning and Genetic Engineering of Insulin
=> Obesity and Leptin
=> A Multitude of Genes Affect Obesity
=> Fat Degradation
=> Monoamine Oxidase and Violent Crime

Aging and Apoptosis


=> Aging and Apoptosis
=> Aging and Apoptosis: Cellular Senescence
=> Factors That Activate Senescence
=> Links between Cancer and Aging
=> Telomeres Shorten during Aging
=> Mitochondria and Aging
=> Life Span and Metabolism in Worms
=> Sirtuins, Histone Acetylation, and Life Span in Yeast
=> Apoptosis Is Programmed Cell Death
=> Apoptosis Involves a Proteolytic Cascade
=> Mammalian Apoptosis
=> Execution Phase of Apoptosis
=> Corpse Clearance in Apoptosis
=> Control of Apoptotic Pathways in Development
=> Alzheimer’s Disease
=> Programmed Cell Death in Bacteria
=> Using Apoptosis to Treat Cancer

Bacterial Infections


=> Bacterial Infections
=> Molecular Approaches to Diagnosis
=> Virulence Genes Are Often Found on Mobile Segments of DNA
=> Attachment and Entry of Pathogenic Bacteria
=> Iron Acquisition by Pathogenic Bacteria
=> Bacterial Toxins
=> ADP Ribosylating Toxins
=> Cholera Toxin
=> Anthrax Toxin
=> Antitoxin Therapy

Viral and Prion Infections


=> Viral Infections and Antiviral Agents
=> Interferons Coordinate the Antiviral Response
=> 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
=> Using Yeast Prions as Models

Biowarfare and Bioterrorism


=> Biowarfare and Bioterrorism
=> Bacteria Make Lethal Proteins to Kill Other Organisms
=> Germ Warfare among the Lower Eukaryotes
=> History of Human Biological Warfare
=> Biowarfare Expectancy and Expense
=> Important Factors in Biological Warfare
=> Which Disease Agents Are Suitable for Biological Warfare?
=> Anthrax
=> The 2001 Anthrax Attack in the United States
=> Other Bacterial Agents
=> Smallpox Virus
=> Other Viral Agents
=> Purified Toxins as Biowarfare Agents
=> Botox-Botulinum Toxin
=> Ribosome Inactivating Proteins
=> Agricultural Biowarfare
=> Genetic Engineering of Infectious Agents
=> Creation of Camouflaged Viruses
=> Biosensors and Detection of Biowarfare Agents

Forensic Molecular Biology


=> The Genetic Basis of Identity
=> Blood, Sweat, and Tears
=> Forensic DNA Testing
=> DNA Fingerprinting
=> Using Repeated Sequences in Fingerprinting
=> Using the Polymerase Chain Reaction (PCR)
=> Probability and DNA Testing
=> Use of DNA Evidence
=> Tracing Genealogies by Mitochondrial DNA and the Y Chromosome
=> Identifying the Remains of the Russian Imperial Family

Bioethics in Biotechnology


=> Approach to Bioethics
=> Power, Profit, Poverty, and Access
=> Ignorance, Novelty, and Cultural Viewpoint
=> Possible Dangers to Individuals, Society, or Nature
=> Health Care and Related Issues
=> Interference with the Natural World
=> Altering the Human Germline
=> Knowledge, Identity, and Ideology
=> Long Term Biological Problems



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