Biotechnology Applying the Genetic Revolution

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Biotechnology Applying the Genetic Revolution

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
Alzheimerís 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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