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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
-:- 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
Mahendra Varman Mahendra Varman Mahendra Varman Mahendra Varman Mahendra Varman

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