Omics Technologies and Bio-engineering: Volume 1: Towards Improving Quality of Life

Dedication
Dedication
List of contributors
List of Contributors
About the editors
About the Editors
Contents 1-5
Contents 5-11
Contents 12-17
Contents 18-23
Contents 23-25
Chapter 01
1 Overview and Principles of Bioengineering: The Drivers of Omics Technologies
1.1 Introduction
1.1.1 Science of “Omics”
1.2 Genomics
1.3 Transcriptomics
1.4 Proteomics
1.5 Metabolomics
1.6 Glycomics
1.7 Omics-Driven Bioengineering
1.7.1 Cellular Engineering
1.7.2 Enzyme Engineering
1.7.3 Metabolic Engineering
1.8 Bioinformatics Intervention in Omics
1.9 Applications of Omics
1.9.1 Food and Agriculture Sector
1.9.2 Health Sector
1.9.3 Environmental Sector
1.10 Conclusion
References
Chapter 02
2 Omics Approaches Towards Transforming Personalized Medicine
2.1 Introduction
2.2 Personalized Medicine
2.3 Pharmacogenomics of Various Disorders
2.3.1 Cancer
2.3.2 Cardiovascular Diseases
2.3.3 Infectious Diseases
2.3.4 Immune Disorders
2.4 Applications of Pharmacogenomics
2.4.1 Personalized Medicine
2.4.2 Drug Discovery
2.5 Companion Diagnostics
2.6 Limitations of Pharmacogenomics
2.7 Future Prospects
2.8 Conclusion
References
Further Reading
Chapter 03
3 Omics Approaches in Marine Biotechnology: The Treasure of Ocean for Human Betterments
3.1 Introduction
3.2 Impact of Omics on Marine Biotechnology
3.3 Omics-driven Marine Biotechnology
3.3.1 Genomics
3.3.2 Proteomics
3.3.3 Transcriptomics
3.3.4 Nutrigenomics
3.3.5 Metabolomics
3.4 Challenges and Future Opportunities
3.4.1 Marine Food
3.4.2 Marine Energy
3.4.3 Human Health
3.5 Conclusion
References
Chapter 04
4 Synthetic Biology: Overview and Applications
4.1 Introduction
4.2 History
4.3 Biology and Chemistry
4.3.1 Cell
4.3.2 Animal Cell
4.3.3 Plant Cell
4.3.4 Function of a Cell
4.3.5 Chemistry
4.3.6 Chemical Composition of a Cell
4.4 Craft and Design
4.4.1 Engineering
4.4.2 Synthetic Morphology
4.4.3 Synthetic Chemistry
4.4.4 Minimal Cell
4.4.5 Rewriting
4.5 Technology
4.5.1 Polypeptides and Proteins
4.5.2 Polynucleotides and DNA and RNA
4.5.3 Restriction Endonucleases
4.5.4 DNA Amplification and Sequencing
4.5.5 DNA and Protein Transfer
4.5.6 Systems Biology
4.5.7 Measurements and Calculations
4.6 Applications
4.6.1 Fundamental and Applied Synthetic Biology
4.6.2 Artificial Life
4.6.3 Biosensor
4.6.4 Synthetic Biological Circuits
4.6.5 Industrial Scale Applications
4.7 Examples
4.7.1 Synthetic Biology Today
4.7.2 Applications
4.7.3 iGEM
4.8 Ethics and Safety
4.8.1 Society, Ethics, and Synthetic Biology
4.8.2 Safety Regulations
4.8.3 Safe Human Practices
4.8.4 Technology Transfer
4.9 Conclusions and Future Perspectives
4.9.1 Promises of Synthetic Biology
4.9.2 Challenges
References
Weblinks
Chapter 05
5 Reverse Engineering and Its Applications
5.1 Introduction
5.2 Applications of Reverse Engineering
5.2.1 Medical Device Design
5.2.2 Pharmaceutical Product Design
5.2.3 Reverse Engineering in Therapeutic Peptide Production
5.2.4 Reverse Engineering in Bioinformatics
5.2.5 Reverse Engineering in Biosystems
5.2.6 Reverse Engineering in Software Design
5.2.7 Reverse Engineering of Software
5.2.8 Reverse Engineering Human Regulatory Networks
5.3 Laws, Economics, and Ethics Governing Reverse Engineering
5.4 Conclusion
5.4 Future Direction
References
Further Reading
Chapter 06
6 Omics Approaches in Forensic Biotechnology: Looking for Ancestry to Offence
6.1 Introduction
6.2 Importance of Omics Approaches in Studying DNA
6.2.1 The DNA
6.2.2 The Genomic Approach
6.2.3 The Transcriptomic Approach
6.2.4 The Proteomics Approach
6.2.5 The Metabolomics Approach
6.2.6 The Toxicogenetics/Pharmacogenetics Approach
6.3 Ancestry and Phylogeny
6.4 DNA Fingerprinting
6.4.1 History
6.4.2 What is DNA Profiling?
6.4.3 Sample Collection From the Suspect
6.4.4 The Process of DNA Extraction
6.4.5 Various Techniques and Analysis Employed in DNA Profiling
6.4.5.1 Dideoxy Method
6.4.5.2 Single Nucleotide Polymorphisms
6.4.5.3 Variable Number Tandem Repeats/Minisatellites
6.4.5.4 STRs/Microsatellites
6.4.5.5 Restriction Fragment Length Polymorphisms
6.4.5.6 Analysis of Degraded or Low Template DNA
6.5 Studying Parenthood
6.5.1 Mitochondrial DNA Analysis
6.5.2 Y-Chromosome Analysis
6.5.3 Forensic DNA Phenotyping
6.6 Application of Omics in Criminology
6.6.1 DNA Databases
6.7 Conclusion
References
Further Reading
Chapter 07
7 Biotechnology and Bioengineering in Astrobiology: Towards a New Habitat for Us
7.1 Introduction to Astrobiotechnology and Astrobioengineering
7.2 Biotechnological Approaches in Detecting Life in Space
7.3 Integration of Biotechnology and Astrobiology
7.4 Advanced Integrated Technologies in Astrobiology for Finding Adequate Habitat Conditions
7.4.1 Proteins (Antibodies)-Based Approaches
7.4.2 Microfluidics
7.4.3 Microarray Technology
7.5 Solar System Exploration
7.6 Conclusion and Future Prospects
References
Further Reading
Chapter 08
8 Lab-on-a-Chip Technology and Its Applications
8.1 Introduction
8.1.1 Diagnostics
8.1.1.1 DNA Extraction and Purification on LOC Devices
8.1.1.2 PCR, qPCR, and Molecular Detection on LOC Devices
8.1.2 Genomic Application
8.1.3 Microarray
8.1.4 Biochemical Applications
8.1.5 Proteomics
8.1.6 Biosensors
8.1.7 Cell Research
8.1.8 Drug Development
8.2. Conclusion and Future Directions
References
Further Reading
Chapter 09
9 Robotics and High-Throughput Techniques
9.1 Introduction
9.1.1 Technologies in Biorobotics
9.1.2 Soft Robotics
9.1.2.1 Structure
9.1.2.2 Bio-inspired Soft Robots
9.1.2.3 Advantages
9.2 Wonders in the Field of Biorobotics
9.2.1 Techniques Used in Biorobotics
9.2.1.1 Electromyography
9.2.1.2 Electroencephalography: Brain–Computer Interfaces or Brain–Machine Interfaces
9.2.1.3 Hybrid EEG–EMG Control Interface
9.2.1.4 Plant Roots–Inspired Robotic Solutions: The PLANTOID Robot
9.2.1.5 Sperm-driven Micro-Biorobot
9.2.1.6 Robotic Cell Injection
9.2.1.7 Biorobotics in Medicine
9.2.1.8 Natural Orifice Surgery Through Biorobotics
9.3 Future Perspective
References
Further Reading
Chapter 10
10 3D Printing Technologies and Their Applications in Biomedical Science
10.1 Introduction
10.2 Types of Printers
10.2.1 Stereolithography
10.2.1.1 Parts of Stereolithographic Machine
10.2.2 Fused Deposition Modeling
10.2.3 Inkjet Printing
10.2.4 Selective Sintering Printing
10.2.5 Laminated Object Manufacturing
10.3 Application of 3D Printing
10.3.1 Craniofacial Plastic Surgery
10.3.2 Skull Reconstruction
10.3.3 Cranioplasty for Correction of Syndromic Craniosynostosis
10.3.4 Facial Bone Fractures
10.3.5 Mandibular Reconstruction
10.3.6 Human Skin
10.3.7 Tissue Engineering
10.3.8 Ears
10.3.9 Cartilage
10.3.10 Heart Valve
10.3.11 Tooth and Peridontal Regeneration
10.4 Oncology and 3D Printing
10.4.1 Cancer Microenvironment Engineering for In Vitro 3D models
10.5 Future Directions
References
Chapter 11
11 Next-Generation Sequencing and Data Analysis: Strategies, Tools, Pipelines and Protocols
11.1 Introduction
11.2 Sequencing Platforms
11.2.1 Illumina Platform
11.2.2 Ion Torrent Platform
11.2.3 PacBio Platform
11.3 Structural Genomics
11.3.1 De Novo Assembly
11.3.2 Reference Assembly
11.3.3 Genome Annotation
11.4 Functional Genomics
11.4.1 RNA-Seq: De Novo and Reference-Based Approaches
11.4.2 ChIP-Seq
11.5 Protocols and Pipelines for Metagenomic Analysis
11.5.1 Analysis of the Microbial Diversity Through PCR Targeting 16S rRNA Genes
11.5.2 Whole-Genome Metagenomic Analysis
11.5.3 Obtaining Genomes From Metagenomic Data
11.6 Future Directions
References
Chapter 12
12 Computational Techniques in Data Integration and Big Data Handling in Omics
12.1 Introduction
12.2 Big Data Concept
12.3 The Three V’s
12.3.1 Volume
12.3.2 Velocity
12.3.3 Variability in Data Origin
12.4 Big Data on Computational Biology Applications
12.5 Tools for Analysis
12.6 Future Direction About Big Data
References
Chapter 13
13 Bioinformatics and Systems Biology in Bioengineering
13.1 Bioinformatics and Major Databases
13.2 Systems Biology—A Brief Overview
13.2.1 Mathematical Representations and Modeling
13.3 Reverse Engineering of Network Interactions
13.3.1 Correlation
13.3.2 Information Theory
13.3.3 Bayesian Inference
13.4 Bioengineering and Systems Biology
13.4.1 Synthetic Biology
13.4.2 Tissue Engineering
13.5 From Biological Networks to Modern Therapeutics
13.5.1 Disease Modeling
13.5.2 Drug Modeling
13.6 Bioinformatics Tools and Resources
13.7 Future Advancements
13.8 Conclusion
References
Chapter 14
14 Techniques for Nucleic Acid Engineering: The Foundation of Gene Manipulation
14.1 Nucleic Acid Isolation Techniques
14.1.1 Introduction
14.1.2 Basics of Nucleic Acid Isolation: A Brief Introduction
14.1.3 Components of Nucleic Acid Isolation
14.1.3.1 Cell Disruption (Cell Lysis)
14.1.3.1.1 Chemical Lysis
14.1.3.1.2 Mechanical Lysis: Methods Involve Grinding, Shearing, Beating, and Shock
14.1.3.2 Removal of Artifacts
14.1.3.3 Precipitation
14.1.3.4 Washing and Resuspension
14.1.4 Principles of Methods of Extraction
14.1.4.1 Organic Methods
14.1.4.1.1 Phenol–Chloroform Method
14.1.4.1.2 Guanidinium Thiocyanate–Phenol–Chloroform Method (Commercial Names: TRI, TRIzol)
14.1.4.1.3 Cetyltrimethylammonium Bromide Method
14.1.4.2 Inorganic Methods
14.1.4.2.1 Salting-Out Method
14.1.4.2.2 Cesium Chloride Density Gradient Method
14.1.4.3 Solid-Based Extraction Method
14.1.4.3.1 Silica-Based Purification
14.1.4.3.2 Magnetic Separation
14.1.4.3.3 Anion Exchange Purification
14.1.4.3.4 FTA Technology (Trademark of General Electric Company): A Fast Technology for Analysis of Nucleic Acids
14.1.5 Automation and High-Throughput Technology
14.1.6 Choosing the Method
14.1.6.1 Genomic DNA Isolation
14.1.6.2 RNA Isolation
14.1.6.3 Plasmid DNA Isolation
14.1.6.4 Mitochondrial DNA Isolation
14.1.6.5 Viral DNA/RNA Isolation
14.1.6.6 Plant DNA/RNA and Chloroplast DNA Isolation
14.1.6.7 DNA/RNA Isolation From Other Materials
14.1.6.7.1 Paraffin Blocks
14.1.6.7.2 Ancient Bone DNA Isolation
14.1.7 Quality Control
14.1.7.1 Agarose Gel Electrophoresis Control
14.1.7.1.1 Checking GDNA
14.1.7.1.2 Checking Total RNA
14.1.7.2 Spectrophotometry
14.1.7.3 Microfluidics-Based High-Throughput Technology
14.1.8 GLP for Nucleic Acid Isolation
14.1.8.1 A Room of Its Own
14.1.8.2 Sampling
14.1.8.3 Extraction
14.1.8.4 Post Processes
14.1.9 Conclusion and Future Perspectives
14.2 Restriction Enzyme Techniques
14.2.1 The Discovery of Restriction Enzymes (Endonucleases)
14.2.2 Where Are They Found?
14.2.3 Mechanism of Their Action
14.2.4 Classification of Restriction Enzyme Types
14.2.4.1 Infidelity Among the Restriction Enzymes
14.2.5 Examples of Restriction Enzymes
14.2.5.1 Sticky-End (Cohesive) Cutters
14.2.5.2 Blunt-End Cutters
14.2.5.3 Utilization of Restriction Enzymes in Biotechnology
14.2.5.4 Detecting SNPs (PCR Restriction Fragment Length Polymorphism)
14.2.5.5 Gene Cloning
14.2.5.6 DNA Footprinting
14.2.5.7 Artificial Restriction Enzymes
14.2.5.8 Restriction Endonuclease Utilization in Diagnostics
14.2.6 Restriction Enzyme Digestion Protocol
14.2.7 Summary
14.3 PCR Techniques
14.3.1 PCR Chronicle
14.3.2 PCR Reaction Components
14.3.2.1 PCR Primer Design
14.3.2.2 PCR Steps
14.3.2.3 PCR Optimization
14.3.2.3.1 PCR Buffer Concentration
14.3.2.3.2 DNA Polymerase Enzyme of Choice
14.3.3 PCR Instrumentation
14.3.3.1 Applied Biosystems
14.3.3.2 Bio-Rad
14.3.3.3 Eppendorf
14.3.4 Recent Advances in PCR Technology and Its Applications
14.3.4.1 Hot Start PCR
14.3.4.2 Reverse Transcriptase PCR
14.3.4.3 Droplet Digital PCR
14.3.4.4 Long PCR
14.3.4.5 Multiplex PCR
14.3.4.6 Colony PCR
14.3.4.7 Nested PCR
14.3.4.8 Quantitative Real-Time PCR
14.3.4.9 PCR Site-Directed Mutagenesis
14.3.4.10 Other PCR Techniques
14.4 Blotting Techniques
14.4.1 General Principle
14.4.1.1 Southern Blotting
14.4.1.1.1 The Order of Sequence of Southern Blot Analysis
14.4.1.1.2 Southern Blot Applications
14.4.1.2 Northern Blotting
14.4.1.2.1 Northern Blot Protocol
14.4.1.2.1.1 RNA Gels
14.4.1.2.2 The Order of Sequence of Northern Blot Analysis
14.4.1.2.3 Applications of Northern Blots
14.4.1.3 Western Blotting
14.4.1.3.1 The Order of Sequence of Western Blot Analysis
14.4.1.3.2 Western Blot Applications
14.4.2 Western Blot Instrumentation
14.4.2.1 Bio-Rad
14.4.2.2 ProteinSimple
14.4.2.3 Life Technologies
14.4.2.4 Additional Blotting Techniques
14.4.2.4.1 Dot Blot
14.4.2.4.2 Reverse Dot Blot
14.4.2.4.2.1 Power of Blotting
14.4.2.4.2.2 Limitations of Blotting
14.5 Recombinant DNA Techniques
14.5.1 Creation of Recombinant (Artificial) DNA
14.5.2 Chimeric/rDNA
14.5.2.1 Steps of Cloning DNA Fragments (Gene Cloning) to Create rDNA
14.5.3 Expression of rDNA
14.5.4 Applications of rDNA Technology
14.5.5 Controversy of rDNA
14.5.6 Genetically Modified Organisms
14.5.7 Genetically Modified Food
14.6 DNA Sequencing Technologies
14.6.1 Brief Introduction
14.6.2 First-Generation Sequencing Techniques
14.6.2.1 Maxam’s and Gilbert’s Chemical Method
14.6.2.2 Sanger Sequencing
14.6.3 Automation in DNA Sequencing
14.6.4 Developments and High-Throughput Methods in DNA Sequencing
14.6.4.1 Pyrosequencing Method
14.6.4.2 The Genome Sequencer 454 FLX System
14.6.4.3 Illumina/Solexa Genome Analyzer
14.6.5 Transition Sequencing Techniques
14.6.5.1 Ion-Torrent’s Semiconductor Sequencing
14.6.5.2 Helico’s Genetic Analysis Platform
14.6.6 Third-Generation Sequencing Techniques
14.7 Conclusion
References
Chapter 15
15 Techniques for Protein Analysis
15.1 Protein Identification
15.1.1 Sequencing
15.1.1.1 Determining Amino Acid Composition With Hydrolysis
15.1.1.2 Quantitative Analysis
15.1.2 Edman Degradation
15.1.2.1 The Edman Degradation Reaction
15.1.2.2 Limitations of the Edman Degradation
15.1.3 Gel Electrophoresis
15.1.3.1 Polyacrylamide Gel Electrophoresis
15.1.3.2 Isoelectric Focusing
15.1.3.3 Two-Dimensional Gel Electrophoresis
15.1.4 Isotope Labeling
15.1.4.1 Enzymatic Labeling
15.1.4.2 Isotope-Coded Affinity Tag
15.1.4.3 Stable-Isotope Labeling in Cell Culture
15.1.5 Mass Spectrometry
15.1.5.1 Principle and Instrumentation
15.1.5.2 Components of the Instrument
15.1.5.2.1 Device for Sample Input Into the Machine
15.1.5.2.2 Molecular Ionization Source
15.1.5.2.3 Mass Analyzer
15.1.5.2.4 Detector
15.1.5.2.5 Vacuum System and Computer-Based Data Obtaining and Processing System
15.1.5.3 Liquid Chromatography–Mass Spectrometry
15.1.5.4 Matrix-Assisted Laser Desorption/Ionization-Time-of-Flight Mass Spectrometry
15.1.5.5 Tandem Mass Spectrometry
15.1.6 Enzyme-Linked Immunosorbent Assay
15.1.6.1 Indirect ELISA
15.1.6.2 Sandwich ELISA
15.1.6.3 Competitive ELISA
15.1.6.4 Reverse ELISA
15.1.7 Immunohistochemistry
15.1.7.1 Sample Preparation
15.1.7.2 Sample Labeling
15.1.7.3 Sample Visualization
15.1.7.4 Applications
15.2 Protein Structural Analysis
15.2.1 Circular Dichroism
15.2.2 Nuclear Magnetic Resonance Spectroscopy
15.2.3 X-Ray Crystallography
15.2.4 Electron Microscopy
15.3 Protein Purification
15.3.1 Chromatography
15.3.1.1 Column Chromatography
15.3.1.2 Size-Exclusion (Gel-Filtration) Chromatography
15.3.1.3 Ion-Exchange Chromatography
15.3.1.4 Affinity Chromatography
15.3.1.5 Reverse Phase High-Performance Liquid Chromatography
15.4 Protein Quantitation With Western Blotting
15.4.1 Tissue Preparation
15.4.2 Gel Electrophoresis
15.4.3 Transfer Methods
15.4.4 Blocking Buffers
15.4.5 Detection
15.4.5.1 Colorimetric Detection
15.4.5.2 Chemiluminescent Detection
15.4.5.3 Radioactive Detection
15.4.5.4 Fluorescent Detection
15.4.6 Protein Microarray
15.4.6.1 Analytical Microarray
15.4.6.2 Functional Protein Microarray
15.4.6.3 Reverse Phase Protein Array
15.5 Conclusion
References
Chapter 16
16 Engineering Monoclonal Antibodies: Production and Applications
16.1 Introduction
16.2 Structures and Functions of Antibodies
16.2.1 Polyclonal Antibodies
16.2.2 Monoclonal Antibodies
16.2.2.1 Production of Monoclonal Antibodies
16.2.2.1.1 Monoclonal Antibody Production by Hybridoma Technique
16.2.2.1.2 Monoclonal Antibody Production by Phage-Display Technique
16.2.2.1.3 Monoclonal Antibody Production Using Transgenic Animals
16.2.2.1.4 Production of Antibodies in Transgenic Plants
16.3 Clinical Usage of the Antibodies
16.3.1 Antibodies in Diagnosis
16.3.1.1 ELISA
16.3.1.2 Western Blotting
16.3.1.3 Flow Cytometric Analyses
16.3.1.4 Immunhistochemistry
16.3.1.4.1 Tissue Preparation
16.3.1.4.2 Antigen Retrieval
16.3.1.4.3 Detection Methods
16.3.1.5 Immunoelectrophoresis
16.3.1.6 Immunodiffusion
16.3.2 Antibodies in Treatment
16.3.2.1 Hematology/Oncology
16.3.2.2 Transplantation
16.3.2.3 Cardiology
16.3.2.4 Infection
16.3.2.5 Rheumatology
16.3.2.6 Gastroenterology
16.3.2.7 FDA-Approved Monoclonal Antibodies
16.4 Conclusion
References
Weblinks
Chapter 17
17 Cell and Tissue Culture: The Base of Biotechnology
17.1 Introduction
17.2 Cell Culture Laboratory
17.2.1 Safety
17.2.2 Cell Culture Equipment and Laboratory Design
17.2.3 Aseptic Technique
17.2.4 Cross Contamination
17.2.5 Biological Contamination
17.3 Cell Culture
17.3.1 Cell Culture System
17.3.2 Cell Line and Culture Monitoring
17.3.3 Primary Culture
17.3.4 Cell Isolation
17.3.5 Culture Environment
17.3.6 Cell Morphology
17.3.7 Cells
17.3.8 Stem Cells
17.4 Methods
17.4.1 Growth and Maintenance of Cells in Culture
17.4.2 Subculturing Adherent Cells
17.4.3 Subculturing Suspension Cells
17.4.4 Viability and Proliferation Assay of Cultured Cells
17.4.5 Freezing Cells (Cryopreservation)
17.4.6 Thawing Frozen Cells
17.4.7 Transplantation of Cultured Cells
17.4.8 Differentiation of Cells
17.4.9 Characterization of Cells
17.4.10 Apoptosis, Necrosis, Senescence, and Quiescence
17.4.11 Senescence
17.4.12 Quiescence
17.4.13 Production From Cell Culture
17.5 Conclusion
References
Chapter 18
18 In Vitro and In Vivo Animal Models: The Engineering Towards Understanding Human Diseases and Therapeutic Interventions
18.1 Introduction
18.2 Mouse Model
18.2.1 LDLR−/− Mice
18.2.2 ApoE−/− Mice
18.2.3 Transgenic Mice of Cardiovascular Diseases
18.2.4 Diabetes-Accelerated Atherosclerosis Mouse Model
18.2.5 Calcium Chloride–Induced AAA
18.2.6 Spontaneous Mouse Mutants
18.2.7 Mouse Model for Liver Metastases
18.2.8 Mouse Model of Colon Cancer
18.2.9 Mouse Model of Fatty Liver Disease
18.2.10 Mouse Models for Neurodegenerative Diseases
18.2.11 Primary Neuronal Cultures and Neuronal Cell Lines
18.2.12 Primary Microglia Cultures
18.2.13 Transgenic Mouse of PD
18.2.14 Transgenic Mouse Model for Alzheimer’s Disease
18.2.15 Animal Models of Heart Failure
18.2.15.1 Localized Aortic Perfusion With Elastase
18.2.15.2 Decellularized Xenografts
18.3 Rat Models
18.3.1 Rat Models for Celiac Disease
18.3.2 Nile Grass Rats
18.4 Porcine Models
18.4.1 Gottingen Miniature Pig Model
18.4.2 Transgenic Huntington Disease Minipigs
18.4.3 Transgenic Pig Model of Amyotrophic Lateral Sclerosis
18.4.4 Pig Models for Ataxia Telangiectasia
18.4.5 Pig Models for Myocardial Infarction
18.5 Zebrafish Model
18.5.1 Zebrafish Models of Epilepsy
18.5.2 Zebrafish Model of AD
18.5.3 Zebrafish Model of PD
18.6 Rabbit Models
18.6.1 Rabbit Model of Inflammation-Associated Atherosclerosis
18.6.2 Rabbit Model for Myocardial Damage
18.7 Conclusion
References
Further Reading
Chapter 19
19 Medical Biotechnology: Techniques and Applications
19.1 Introduction
19.2 Background of Medical Biotechnology
19.2.1 Techniques
19.2.1.1 Polymerase Chain Reaction
19.2.1.2 Fluorescence In Situ Hybridization
19.2.1.3 Sequencing
19.2.1.4 Microarrays
19.2.1.5 Cell Culture
19.2.1.6 Interference RNA
19.2.1.7 Genome Editing
19.2.2 Emerging Trends
19.2.2.1 Stem Cells
19.2.2.2 The Human Genome Project
19.2.2.3 Recombinant DNA Technology
19.3 Products of Medical Biotechnology
19.3.1 Antibiotics
19.3.2 Recombinant Proteins
19.3.3 Hybridoma and MAb
19.3.4 Vaccines
19.3.5 Stem Cell Therapy
19.3.6 Tissue Engineering
19.4 Conclusion
References
Chapter 20
20 Tissue Engineering: Towards Development of Regenerative and Transplant Medicine
20.1 Introduction
20.2 Types of Cells (Proliferation and Differentiation)
20.3 Scaffolds
20.3.1 ECM Scaffolds
20.3.2 Natural Biomaterials
20.3.3 Synthetic Biomaterials
20.3.4 Scaffold-Free Strategies
20.4 Biomolecules Importance in Tissue Engineering
20.5 Assembly Methods of a Tissue Culture and Its Maintenance
20.5.1 Engineering Design Aspects
20.5.2 Biomechanical Aspects of Design (Bioreactors)
20.6 Regeneration of a Damaged Tissue Using Tissue Engineering
20.6.1 Blood Vessels
20.6.2 Skin
20.6.3 Bone and Cartilage
20.6.4 Cardiovascular Diseases
20.7 The Formation of Bioartificial Organs Using Cell-Based Tissue Engineering
20.7.1 Liver
20.7.2 Bladder
20.7.3 Kidney
20.8 Cell Therapies in Tissue Engineering
20.9 Use of Stem Cells and Therapeutic Cloning in Tissue Engineering
20.10 Aid of Nanotechnology in Tissue Engineering
20.11 The Challenges of Tissue Engineering
20.12 Conclusion and Future Prospects
20.12.1 Conclusion
References
Chapter 21
21 Therapeutic Aspects of Stem Cells in Regenerative Medicine
21.1 Introduction
21.2 Characteristics of Stem Cells Suitable for Regenerative Medicine
21.3 Policies of United States and Other Nations in the Field of Stem Cell Research
21.4 Stem Cells in Regenerative Medicine of Different Diseases
21.4.1 Spinal Cord Injuries
21.4.2 Heart and Vascular System
21.4.3 Periodontal Diseases
21.4.4 Ocular Diseases
21.4.5 Diabetes
21.4.6 Skin Wounds and Burns
21.4.7 Ischemic Limb Disease
21.4.8 Bone, Cartilage, and Muscle-Related Abnormalities
21.4.9 Neurological Disorder
21.4.10 Cancers
21.4.11 Liver Injury and Cirrhosis
21.4.12 Muscular Dystrophy
21.5 Challenges in Stem Cell Research
21.6 Concluding Remarks
References
Chapter 22
22 Genetic Engineering: Towards Gene Therapy and Molecular Medicine
22.1 Introduction: Gene Therapy and Molecular Medicine
22.1.1 Germinal Gene Therapy
22.1.2 Somatic Gene Therapy
22.2 Historical Significance
22.3 Gene Transfer Strategy: Delivery Vehicle
22.3.1 Viral Vectors: Gene Therapy
22.3.1.1 Retroviral Vectors
22.3.1.2 Adenovirus-Based Vectors
22.3.2 Nonviral Vectors: Liposome
22.4 Clinical Trials (In Vivo and Ex Vivo): An update
22.5 Gene Therapy and Disease/Disorders
22.5.1 Gene Therapy and Hemophilia
22.5.2 Gene Therapy and Cardiovascular Disorders
22.5.2.1 Angiogenic Gene Therapy
22.5.2.2 Non-Angiogenic Gene Therapy
22.5.2.3 Combination Therapy
22.5.3 Gene Therapy and Diabetes
22.5.4 Gene Therapy and Neurological Disorders
22.5.4.1 Parkinson’s Disease
22.5.4.2 Alzheimer’s disease
22.5.5 Gene Therapy and HIV Infection
22.5.5.1 Genetic Approaches to Inhibit HIV Replication
22.5.5.2 Transdominant Negative Proteins
22.5.5.3 Single-Chain Antibodies (Intrabodies)
22.5.5.4 Endogenous Cellular Proteins as Anti-HIV Agents
22.5.5.5 Nucleic Acid–Based Gene Therapy Approaches: RNA Decoys
22.5.5.6 Antisense DNA and RNA
22.5.5.7 Ribozymes (Catalytic Antisense RNA)
22.5.5.8 DNA Vaccines
22.5.5.9 HIV-Specific Cytotoxic T Lymphocytes
22.5.6 Gene Therapy and Various Cancers
22.5.6.1 Gene Therapy and Hematological Malignancy
22.5.6.2 Gene Therapy and Oral Cancer
22.5.6.3 Gene Therapy and Breast Cancer
22.5.6.4 Gene Therapy and Ovarian Cancer
22.5.6.5 Gene Therapy and Lung Cancer
22.5.6.6 Gene Therapy and Prostate Cancer
22.6 Obstacles and Barriers
22.6.1 Activation and Delivery of Gene
22.6.2 Controlled Gene Expression
22.6.3 Activation of Immune Response
22.6.4 Commercially Unviable
22.6.5 Safety Issues
22.7 Conclusions and Future Prospective
References
Chapter 23
23 Biotechnology for Biomarkers: Towards Prediction, Screening, Diagnosis, Prognosis, and Therapy
23.1 Introduction
23.2 Evolution of Biomarkers
23.3 Classification of Biomarkers
23.3.1 Susceptibility Biomarkers
23.3.1.1 Infectious Diseases
23.3.1.2 Cardiovascular Diseases
23.3.1.3 Rheumatoid Arthritis
23.3.2 Diagnostic and Prognostic Biomarkers
23.3.2.1 Cancer
23.3.2.2 Rheumatoid Arthritis
23.3.3 Therapeutic Biomarkers
23.3.3.1 Infectious Diseases
23.3.3.2 Cardiology
23.3.3.3 Rheumatoid Arthritis
23.4 Food and Drug Administration–Approved Biomarkers
23.5 Biomarkers for Drug Discovery and Development
23.6 Regulatory Issues
23.7 Future Prospects
23.8 Conclusion
References
Further Reading
Chapter 24
24 Omics Approaches in In Vitro Fertilization
24.1 Introduction
24.2 Historical Aspects
24.3 Human IVF
24.4 Benefits of IVF
24.5 Omics Approaches in IVF
24.5.1 Genomics in IVF
24.5.2 Transcriptomics in IVF
24.5.3 Proteomics in IVF
24.5.4 Metabolomics in IVF
24.5.5 Pharmacogenomics of IVF
24.6 Techniques and Protocols Involved in Different Steps of IVF and Embryo Transfer
24.7 Variations of IVF
24.8 Success Rates of IVF
24.9 Complications of IVF
24.10 Cost and Convenience
24.10.1 Clinical Factors
24.10.2 Patient Factors
24.10.3 Medications
24.10.4 Precycle Costs
24.10.5 Cycle Costs
24.10.5.1 Embryo Freezing Costs
24.11 Challenges and Issues
24.11.1 Ethical
24.11.2 Social
24.11.3 Religious
24.11.4 Psychological and Emotional
24.12 Legal Issues
24.13 Conclusion and Future Prospective
References
Chapter 25
25 Safety and Ethics in Biotechnology and Bioengineering: What to Follow and What Not to
25.1 Introduction
25.1.1 Addressing Ethical Issues
25.1.2 Organizations Framing Research Ethics in Biotechnology and Bioengineering
25.1.3 Ethical Concern in Agriculture
25.1.3.1 Sustainable Agriculture
25.1.3.2 Transgenic Plants
25.1.4 Impact of Biotechnology and Bioengineering on Animals
25.1.4.1 Transgenic Animals
25.1.5 Ethical Concerns of Xenotransplantation
25.1.6 Ethical Issues in Stem Cell Research
25.1.7 Ethical Issues in Aquaculture Industry
25.1.8 Ethics in Biobanking
25.1.8.1 Biosafety Issues of Modern Biotechnology and Bioengineering
25.1.8.2 Adverse Effect on Health of People/Environment
25.1.8.3 Unpredictable and Unintended effects
25.1.8.4 Impacts on Socioeconomic Welfare of Countries and of Communities
25.1.8.5 Impact of Traditional Values and Culture
25.1.8.6 Ethical Issues in Medical Biotechnology
25.1.8.7 Protecting Human Beings in Clinical Trials
25.1.8.8 Accountability
25.1.8.9 Affordability
25.1.8.10 Privacy
25.1.8.11 Intellectual Property Rights
25.2 Conclusion
References
Further Reading
Index
Index