Fisheries Biotechnology and Bioinformatics

Preface
Contents
About the Authors
1: Biotechnology in Fisheries
1.1 Biotechnology
1.2 Concepts and Terminologies in Biotechnology
1.3 Fields of Biotechnology
1.3.1 Agricultural Biotechnology
1.3.2 Animal Biotechnology
1.3.3 Industrial Biotechnology
1.3.4 Environmental Biotechnology
1.3.5 Fisheries Biotechnology
1.4 Significant Developments in the Field of Biotechnology
1.5 Significant Developments in Fisheries Biotechnology
Reference
2: Nucleic Acids
2.1 Components of Nucleic Acid
2.1.1 Nitrogenous Bases
2.1.2 Pentose Sugar
2.1.3 Phosphoric Acid
2.2 Nucleoside and Nucleotide
2.3 Polynucleotide or Nucleic Acid Strand
2.4 DNA as Genetic Material
2.4.1 DNA Structure
2.4.1.1 The Double Helix
2.4.1.2 Minor and Major Grooves
2.4.1.3 Conformations
Syn Conformation
Endo and Exo Conformation
2.4.2 Different Forms of DNA
2.4.2.1 B-DNA
2.4.2.2 A-DNA
2.4.2.3 Z-DNA
2.4.2.4 Conditions Favoring A-Form, B-Form, and Z-Form of DNA
2.5 Ribonucleic Acid (RNA)
2.5.1 Chemical Structure of RNA
2.5.2 Types of RNA
2.5.2.1 Messenger RNA (mRNA)
2.5.2.2 Transfer RNA (tRNA)
2.5.2.3 Ribosomal RNA (rRNA)
2.6 Difference Between DNA and RNA
References
3: Genes and Genetic Codes
3.1 Genes
3.1.1 Activities of Genes
3.1.2 Structure of Gene
3.1.3 Types of Genes Based on Their Function and Position
3.2 Genetic Code
3.2.1 Discovery of the Genetic Code
3.2.2 Codons and Amino Acids
3.2.2.1 START and STOP Codons
3.2.3 Properties of the Genetic Code
3.2.4 The Wobble Hypothesis
3.2.4.1 Wobble Base Pairs
3.2.4.2 Significance of the Wobble Hypothesis
References
4: Mutations and Their Implications
4.1 Effects of Mutations
4.2 Types of Mutations
4.2.1 Gene Mutations
4.2.1.1 Spontaneous Mutations
Base Pair Substitution
Silent Mutations
Neutral Mutation
Missense Mutation
Nonsense Mutation (Amber Mutations)
4.2.1.2 Frame Shift Mutations/Insertion and Deletion Mutations
4.2.1.3 Transposon Insertion
4.2.2 Chromosomal Mutations (Aberrations)
4.2.2.1 Translocation
4.2.2.2 Inversion
4.2.2.3 Deletion
4.2.2.4 Duplication
4.2.2.5 Polyploidy
5: Gene Expression in Prokaryotes
5.1 Formation of Operon
5.2 Components of Operon
5.3 Structure of Operon
5.4 Functions of Operon
5.5 Lac Operon
5.6 Trp Operon
References
6: Gene Expression in Eukaryotes
6.1 DNA Replication, Transcription, and Translation
6.1.1 Replication
6.1.1.1 Origin of Replication
6.1.1.2 Replication Fork
6.1.1.3 Leading and Lagging Strands
6.1.1.4 Types of Replication
6.1.2 Transcription
6.1.2.1 Initiation
6.1.2.2 Elongation
6.1.2.3 Termination
6.1.2.4 Processing the mRNA Transcript
6.1.3 Translation
6.1.3.1 Initiation
6.1.3.2 Elongation
6.1.3.3 Termination
References
7: Epigenetics
7.1 Covalent Modification of DNA: Cytosine Methylation
7.2 Methylation Regulates Transcription Through Multiple Mechanisms
7.3 DNA Methylation in Fishes
7.4 Histone Modifications
7.4.1 Acetylation
7.4.2 Methylation
7.4.3 Ubiquitination
7.4.4 Phosphorylation
7.4.5 Histone Post-translational Modifications in Fish
References
Untitled
8: RNA in Gene Regulation
8.1 Antisense RNA
8.1.1 Small Interfering RNA
8.1.2 Micro RNAs
8.1.3 lncRNAs
8.1.4 piRNAs
8.1.5 Ribozymes
References
9: Recombinant DNA Technology
9.1 Enzymes
9.1.1 Restriction Enzymes
9.1.2 DNA Polymerase
9.1.3 Taq DNA Polymerase
9.1.4 Reverse Transcriptase
9.1.5 DNA Ligase
9.2 Vectors
9.2.1 Plasmids
9.2.2 Types of Cloning Vectors
9.2.2.1 Shuttle Vectors
9.2.2.2 Bacteriophages as Cloning Vectors
9.2.2.3 Cosmids
9.2.2.4 Yeast Cloning Vectors
9.2.2.5 Expression Vectors
9.3 Host Organism
9.4 Steps Involved
9.4.1 Isolation of the Genetic Material
9.4.2 Cutting of DNA at Specific Locations
9.4.3 Isolation of Desired DNA Fragment
9.4.4 Amplification of Gene of Interest Using PCR
9.4.5 Ligation of DNA Fragment into a Vector
9.4.6 Insertion of Recombinant DNA into the Host Cell
9.4.7 Culturing the Foreign Gene Product
9.4.8 Cloning Foreign DNA into Plasmid DNA
References
10: Transgenic Fish Production
10.1 Selection of Fish Species
10.2 Preparation of Transgene Constructs
10.3 Isolation of the Gene of Interest
10.3.1 Genes of Interest
10.3.1.1 Growth Hormone (GH) Gene
10.3.1.2 Anti-freeze Protein Genes
10.3.1.3 Disease Resistance
10.4 Cloning the Gene of Interest
10.5 Gene Transfer
10.5.1 Microinjection
10.5.2 Electroporation
10.5.3 Transgenic Mosaicism
10.6 Identification of Transgenic Fish
10.7 Expression of Transgenes
10.8 Inheritance of Transgenes
10.9 Advantages
10.10 Risks
11: Animal Cell Culture
11.1 Types of Animal Cell Culture
11.1.1 Based on the Number of Cell Division
11.1.1.1 Primary Cell Culture
Adherent Cells
Suspension Cells
Confluent Culture and the Necessity of Subculture
11.1.1.2 Secondary Cell Culture and Cell Line
11.1.2 Based on the Life Span of Culture
11.1.2.1 Finite Cell Lines
11.1.2.2 Continuous Cell Lines
11.2 Cell Strain
11.2.1 Methods
11.2.1.1 Growth Requirements
11.2.1.2 Process to Obtain Primary Cell Culture
11.2.1.3 Aseptic Techniques
11.2.1.4 Cryopreservation
11.3 Applications of Cell Line
11.3.1 Vaccines Production
11.3.2 Virus Cultivation and Study
11.3.3 Cellular and Molecular Biology
11.3.4 Cancer Research
11.3.5 Gene Therapy
11.3.6 Immunological Studies
11.3.7 Others
12: Hybridoma Technology
12.1 Monoclonal Antibodies (MAbs)
12.2 Production of MAb
12.2.1 Steps in Production of MAb
12.2.1.1 Immunization of Mice
12.2.1.2 Screening of Mice for Antibody Production
12.2.1.3 Preparation of Myeloma Cells
12.2.1.4 Fusion of Myeloma Cells with Immune Spleen Cells
12.2.1.5 Isolation and Cloning of Hybridoma Cell with Single Specificity
12.3 Application of Monoclonal Antibodies (MAbs) in Aquaculture
13: Cryopreservation Technology in Fishes
13.1 Diluents
13.1.1 Extenders
13.1.1.1 Types of Extenders
Sugar-Based Extenders
Ionic Extenders
13.1.1.2 Role of Different Salts Used in Extenders
13.1.1.3 Properties of Extender
13.1.1.4 Functions of Extender
13.1.2 Cryoprotectants
13.1.2.1 Chemicals with Cryoprotective Properties
13.1.2.2 Types of Cryoprotectants
Penetrating Cryoprotectants
13.2 Dilution
13.3 Process of Cryopreservation
13.3.1 Selection of Brooders
13.3.2 Milt Collection
13.3.3 Diluent Preparation
13.3.3.1 Dilution Ratio
13.3.4 Equilibration of Milt
13.3.5 Packing of Milt
13.3.6 Pre-freezing
13.3.7 Freezing and Storage
13.3.8 Thawing
13.4 Cryopreservation in Aquaculture
References
14: Molecular Techniques
14.1 Polymerase Chain Reaction (PCR)
14.1.1 Requirements of a PCR Reaction
14.1.2 PCR Cycle
14.1.2.1 Denaturation
14.1.2.2 Annealing
14.1.2.3 Extension
14.1.3 Steps in PCR
14.1.4 Types of PCR
14.1.5 Uses of PCR
14.2 Enzyme-Linked Immunosorbent Assay (ELISA)
14.2.1 ELISA Principle
14.2.2 Requirements for ELISA
14.2.2.1 Enzyme Labels
14.2.3 Stages in ELISA
14.2.4 Methods in ELISA
14.2.5 Types of ELISA Assay
14.2.5.1 Direct ELISA
Advantages
Disadvantages
14.2.5.2 Indirect ELISA
Advantages
Disadvantages
14.2.5.3 Sandwich ELISA
Advantages
Disadvantages
14.3 Blotting Techniques
14.3.1 Southern Blotting
14.3.1.1 Procedure
14.3.1.2 Application
14.3.2 Northern Blotting
14.3.2.1 Procedure
14.3.2.2 Applications
14.3.3 Western Blotting
14.3.3.1 Procedure
14.3.3.2 Applications
14.4 DNA Fingerprinting
14.4.1 Procedure
14.4.2 Application in Fisheries
14.5 DNA Sequencing
14.5.1 Maxam-Gilbert Sequencing
14.5.2 Chain Termination Method
14.5.2.1 Requirements
14.5.2.2 Procedure
14.5.3 Dye-Terminator Sequencing
14.5.4 Pyrosequencing
14.5.5 High-Throughput Sequencing
14.5.5.1 Illumina
14.5.5.2 Ion Torrent
14.5.5.3 Pacific Biosciences
14.5.5.4 Oxford Nanopore Technologies
14.5.6 Applications of DNA Sequencing Technologies (Mardis 2017)
14.6 Protein Sequencing
14.6.1 Protein Sequencing by Edman Degradation
14.6.1.1 Advantages of Edman Degradation
14.6.1.2 Disadvantages of Edman Degradation (Saraswathy and Ramalingam 2011)
14.6.2 Mass Spectrometry (MS)
14.6.3 Applications of Protein Sequencing
References
15: Molecular Markers
15.1 Advantages of Molecular Markers
15.2 Properties of Ideal Genetic Markers
15.3 Types of Markers
15.3.1 Non-PCR-Based Markers
15.3.1.1 Restriction Fragment Length Polymorphism (RFLP)
Principle of RFLP
Steps Involved in RFLP
Applications of RFLP
Advantages of RFLP
Limitations of RFLP
15.3.2 PCR-Based Markers
15.3.2.1 Random Amplified Polymorphic DNA (RAPD)
Advantages
Disadvantages
15.3.2.2 Amplified Fragment Length Polymorphisms (AFLP)
Applications
Advantages of AFLP Marker
Disadvantages of AFLP
15.3.2.3 Microsatellites
Advantages of Microsatellites
Disadvantages of Microsatellites
15.3.3 Sequence-Based Markers
15.3.3.1 Expressed Sequence Tags (ESTs)
Advantages of ESTs
Disadvantages of ESTs
15.3.3.2 Single Nucleotide Polymorphisms (SNPs)
References
16: Biosensor
16.1 Immobilization of Biological Material
16.2 Components of a Biosensor
16.3 Construction of Biosensor
16.3.1 Pre-requisites for Developing Biosensor
16.3.2 Characteristics of Good Biosensor
16.4 Types of Biosensors
16.4.1 Calorimetric Biosensors
16.4.2 Potentiometric Biosensors
16.4.3 Amperometric Biosensors
16.4.4 Optical Biosensors
16.4.5 Acoustic Wave Biosensors
16.5 Applications
16.6 Applications in Fisheries
16.6.1 Biosensors in Food Analysis
16.6.2 Biosensors in Aquatic Environment Assays
16.6.3 Aequorin
16.6.4 Green Fluorescent Protein (GFP)
16.6.5 Biosensors in the Detection of Fish Toxins
16.6.6 Lab-on-a-Fish from PNNL
16.6.7 BIOLAN for Sulfite Testing
References
17: Bioremediation
17.1 Principle of Bioremediation
17.1.1 Factors Determining the Success of Bioremediation
17.1.1.1 Microbial Populations
17.1.1.2 Bio-stimulation
17.2 Bioremediation in Fisheries
17.2.1 Bioremediation Using Algal Mat
17.2.2 Bioremediation Using Bagasse
17.2.3 Bioremediation of Wastewater Using Aquatic Weeds
17.2.4 Bioremediation of Wastewater Using Earthworms
17.2.5 Bioremediation of Spilled Oil
17.2.6 Bioremediation of Organophosphorus Pesticides
17.2.7 Other Bioremediation
17.3 Advantages of Bioremediation
17.4 Disadvantages of Bioremediation
References
18: Bioprospecting in Fisheries
18.1 Phases Involved
18.2 Bioprospecting Marine Biological Resources
18.3 Regulation of Bioprospecting
18.3.1 Bonn Guidelines (Sirakaya 2019)
18.3.2 United Nations Convention on the Law of the Seas (UNCLOS) (Guilfoyle 2019)
18.3.3 Global Ocean Commission (Global Ocean Commission 2014)
18.3.4 International Sea Bed Authority (Jaeckel 2020)
18.3.5 Valencia Declaration (Laladhas et al. 2016)
18.3.6 European Micro B3 (Chege kamau et al. 2015)
18.3.7 European Science Foundation
18.3.8 Nagoya Protocol (Martins et al. 2020)
18.4 Biopiracy
References
19: Bioprocess Engineering in Fisheries
19.1 Stages Involved
19.1.1 Upstream Processing
19.1.1.1 Inoculum Development
19.1.1.2 Medium Preparation
Criteria for Selection of a Medium
19.1.1.3 Criteria for Selection of Raw Materials
19.1.1.4 Inoculum Scale Up
19.1.1.5 Preparation and Sterilization of Media
19.1.2 Reactor Engineering
19.1.2.1 Fermentors
19.1.2.2 Design of Fermentor
19.1.2.3 Fermentation Process
Batch Fermentation
Continuous Fermentation
Fed Batch System
19.1.2.4 Types of Fermentors
Continuous Stirred Tank Bioreactor
Airlift Bioreactor
Packed Bed Bioreactor
Fluidized Bed Bioreactor
Photobioreactor
Membrane Bioreactor
Bubble Column Bioreactors
19.1.2.5 Fermentation Medium
19.1.3 Downstream Processing
19.1.3.1 Initial Considerations and Primary Recovery
Centrifugation and Filtration
Cell Lysis
Recovery of Material from Inclusion Bodies
19.1.3.2 Protein Precipitation
19.1.3.3 Chromatography
Alternatives to Packed Bed Chromatography
19.1.3.4 Design of Biomolecules for Downstream Processing
19.2 Role of Bioprocess Engineering in Fisheries
References
Untitled
20: Bioinformatics: Databases and Formats
20.1 Databases
20.2 Classifications of Databases
20.2.1 Primary Database
20.2.1.1 Types of Primary Database
20.2.2 Secondary Database
20.2.3 Biological Databases
20.2.3.1 Sequence Databases
Nucleotide Databases
Protein Databases
20.3 Tools for Sequence Analysis
20.3.1 BLAST (Basic Local Alignment Search Tool)
20.3.2 CLUSTALW
20.3.3 FASTA
21: Sequence Retrieval, Analysis, and Manipulation
21.1 Sequence Retrieval System
21.1.1 Types of Sequence Retrieval Databases
21.1.1.1 Global Nucleotide Sequence Storage
21.1.1.2 Genome Centered Database
21.1.1.3 Protein Database
21.1.2 Sequence Retrieval in NCBI
21.2 Sequence Analysis
21.2.1 Output of Sequence Analysis
21.2.2 Parameters for Which Sequence Analysis Is Applied
21.2.2.1 Sequence Alignment
Alignment Methods
Dot Plot
21.2.2.2 Profile Comparison
21.2.2.3 Sequence Assembly
21.2.2.4 Gene Prediction
21.2.2.5 Protein Structure Prediction
21.3 Sequence Manipulation Suite
21.3.1 DNA Entry
21.3.2 DNA Manipulation
21.3.3 DNA Figures
21.3.4 DNA Analysis
21.3.5 Protein Entry
21.3.6 Protein Manipulation
21.3.7 Protein Figures
21.3.8 Protein Analysis
22: Bioinformatics Tools and Techniques
22.1 Primer Design
22.1.1 Before Starting
22.1.2 Characteristics of Good Primer
22.1.2.1 Uniqueness
22.1.2.2 Length
22.1.2.3 Base Composition
22.1.2.4 Melting Temperature
22.1.2.5 Annealing Temperature
22.1.3 Good Primer
22.2 Restriction Mapping
22.2.1 Method
22.2.2 Example
22.2.2.1 Digests
22.2.2.2 Resultant Fragments: Approximate Sizes
22.2.2.3 Hypothetical Multiple Cloning Site of Vector
Discussion
Resultant Map
22.3 Orf Finder
22.3.1 Reading Frame
22.3.2 Open Reading Frames
22.3.2.1 Biological Significance
22.3.3 ORF Finding Tools
22.3.3.1 ORF Finder
22.3.3.2 ORF Investigator
22.3.3.3 ORF Predictor
22.3.3.4 ORFik
22.4 EMBOSS
22.4.1 Advantages of EMBOSS
22.4.2 Applications of EMBOSS
22.5 Molecular Visualization
22.5.1 Tools for Molecular Visualization
22.5.1.1 RASMOL
22.5.1.2 Chime
22.5.1.3 Cn3D
22.5.1.4 MolMol
22.6 Benefits of Bioinformatics
22.7 Future Scope
23: Genomics and Its Application in Fisheries
23.1 Application in Aquaculture and Fisheries
23.2 Potential Genomic Technologies for Aquaculture and Fisheries
23.3 Major Aquaculture Genome Projects
23.4 Fish Genome Sequencing
References