Vaccine Design Volume 1 Vaccines for Human Diseases 2nd Edition by Sunil Thomas ISBN B0BTWXB5NH 9781071618844

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ISBN 10: B0BTWXB5NH
ISBN 13: 9781071618844
Author: Sunil Thomas

This volume provides a practical guide providing step-by-step protocol to design and develop vaccines for human diseases. Divided into three volumes, Volume 1: Vaccines for Human Diseases guides readers through an introductory section on future challenges for vaccinologists and the immunological mechanism of vaccines. Chapters focus on design of human vaccines for viral, bacterial, fungal, and parasitic diseases as well as tumor vaccines. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials and reagents, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols.

Authoritative and practical, Vaccine Design: Methods and Protocols, Second Edition, Volume 1: Vaccines for Human Diseases aims to be a useful practical guide to researchers to help further their study in this field.

Vaccine Design Volume 1 Vaccines for Human Diseases 2nd Edition Table of contents:

Part I: Vaccines: Introduction
Chapter 1: Challenges for Vaccinologists in the First Half of the Twenty-First Century
1 Introduction
1.1 Change and Emerging Infectious Diseases
1.2 Development of Vaccines to Protect against COVID-19
1.3 Development of Vaccines to Protect against HIV
2 Development of Vaccines for Flaviviruses
3 Development of Vaccines for Norovirus
4 Development of Vaccines for Influenza
5 Development of Vaccines for Sepsis
6 Development of Vaccines for Tuberculosis
7 Development of Vaccines for Tick-Borne Diseases
8 Development of Vaccines for Flesh-Eating Bacteria
9 Development of Vaccines for Parasites
10 Development of Vaccines for Malaria
11 Development of Vaccines for Cancer, Neurodegenerative Diseases, Substance Abuse, and Autoimmune Diseases
12 Antibody-Dependent Enhancement
13 Future Challenges
References
Chapter 2: Principles in Immunology for the Design and Development of Vaccines
1 Introduction
1.1 A Brief History of Vaccination
2 Basic Concepts of Vaccine Immunology
3 Innate Immunity
4 Adaptive Immunity
5 T Cells
6 B Cells
7 Immune Memory
8 How Do Vaccines Mediate Protection?
9 Immune Correlates of Protection
10 Principles of Vaccine Development
11 Selecting Vaccine Antigens
12 Improving Vaccines
13 Future Prospects
References
Chapter 3: Revisiting the Principles of Designing a Vaccine
1 Introduction
2 Disruption in Antigenic Priming Affects Vaccine Efficacy
2.1 Stage-Specific Vaccine Candidate Imparts Specificity
2.2 Relative Antigen Abundance During Processing Inside APCs
2.3 Subcellular Localization and Availability of Antigens for Processing
3 Leishmania-Associated Inhibitions in Antigenic Processing/Presentation
3.1 Endocytic Mechanisms for Leishmania Uptake
3.2 Inhibition of Phagolysosome Formation
3.3 Dysregulation of Protease Activity by Leishmania
3.4 Destruction of Antigen Presentation Machinery inside Macrophages
3.5 Immunodominance and Epitope Crypticity Affects Vaccination
3.6 Dysfunctional Epitope Loading to MHC Molecule
3.7 MHC-II Affinity Determines the Immunodominant Nature of Generated Epitopes
4 Impairment of Immune Synapse at the APC-T Cell Junction
5 T Cell Associated Events Affecting Vaccination Outcome
5.1 T-Cell Plasticity
5.2 T-Cell Anergy
5.3 T Cell Exhaustion
5.4 Programmed Cell Death or Apoptosis
6 Reverse Vaccinology: An Extension of Immunoinformatics
7 Reverse Vaccinology in T Cell-Based Vaccine Design
7.1 Epitope Prediction and Mapping
7.2 Utility of Comparative Genomics and Pangenome Analysis
7.3 Genome Annotation, Subcellular Localization, and Antigenicity Prediction
8 Reverse Vaccinology Against Leishmaniasis: Redefining Vaccine Candidate Selection
9 Proteomics-Based Approaches for High-Throughput Vaccine Discovery against Leishmaniasis
References
Chapter 4: Status of COVID-19 Pandemic Before the Administration of Vaccine
1 Introduction
2 Origin and Transmission
3 Symptoms Caused by the SARS-CoV-2 Virus
4 Structure of SARS-CoV-2
5 Variants of SARS-CoV-2
6 Immediate Scenario After Partial or Complete Lockdown Due to COVID-19
7 Drugs Used in the Treatment of COVID-19
8 Behavioral Pattern that Slowed the Virus
9 Poor Leadership Impacted the Spread of the Virus Globally
10 COVID-19 in India
11 Distribution of Vaccines
12 Wastage of Vaccines
13 Impact of COVID-19 on Climate Change
14 Preparing for a Pandemic in the Future
References
Part II: Trends in Vaccinology
Chapter 5: mRNA Vaccines to Protect Against Diseases
1 Introduction
2 Nucleic Acid Vaccines Protect Against Infection
3 Development of mRNA as a Vaccine
4 Types of mRNA Vaccines
5 Formulation and Delivery of mRNA Vaccines
6 mRNA Vaccines Against SARS-CoV-2
7 mRNA Vaccines Targeting Influenza
8 mRNA Vaccines Targeting Rabies
9 mRNA Vaccines Against Zika Virus
10 mRNA Vaccines Against Bacterial and Parasite Infections
10.1 mRNA Vaccines Against Cancer
11 Challenges in the Development of mRNA Vaccines
12 Future of mRNA Vaccines
13 Brief History of Katalin Kariko, the Pioneer of mRNA Vaccine Technology
References
Chapter 6: Artificial Intelligence in Vaccine and Drug Design
1 Introduction
2 Use of AI to Determine Protein Structure
3 AI in Drug Design and Vaccine Development
4 Use of AI in Immunological Applications
5 AI in Vaccine Design and Development
6 In Silico Approaches to SARS-CoV-2 Drug and Vaccine Design and Diagnosis
7 Conclusions
References
Part III: Vaccines for Human Viral Diseases
Chapter 7: Vaccines Targeting Numerous Coronavirus Antigens, Ensuring Broader Global Population Coverage: Multi-epitope and Mu…
1 Introduction
1.1 Vaccine Using Whole Coronaviruses as Antigen
1.2 Vaccines Targeting Subunit/Full-Length Proteins of Coronaviruses as Antigen
1.3 Vaccines Targeting Multiple Coronaviruses Proteins
1.3.1 Multi-epitope Vaccine
1.3.2 Multi-patch Vaccine
2 Materials
2.1 Coronavirus Proteomes
2.2 Adjuvants
2.3 Linkers
2.4 Validation Assays
2.5 Purification of Multi-epitope Vaccine and Multi-patch Vaccine Candidates
3 Methods
3.1 Screening of the Coronavirus Proteome for Epitopes and Ag-Patches
3.1.1 Screening for Cytotoxic T Lymphocyte (CTL) Epitopes
3.1.2 Immunogenicity
3.1.3 Screening of Helper T lymphocyte (HTL) Epitopes
3.1.4 Identification of Protein Sequence and Protein Structure-Based B Cell Epitopes
3.1.5 In Vitro Microarray-Based Screening of Epitopes from the Coronavirus Proteome
3.1.6 A Novel “Reverse Epitomics´´ Approach for the Identification of Antigenic Patches (Ag-Patches)
3.1.7 Estimation of Population Coverage by Screened CTL and HTL Epitopes and Identified Ag-Patches
3.2 Epitope Characterization
3.2.1 Conservation Analysis of Epitopes and Antigenic Patches (Ag-Patches)
3.2.2 Epitope Toxicity Prediction
3.2.3 Overlapping Residue Analysis of CTL, HTL, and B Cell Epitopes
3.2.4 In Silico Validation of Shortlisted Epitopes
3.2.5 Molecular Interaction Analysis of Selected CTL Epitopes with TAP Transporter
3.3 In Vitro Epitope-Antibody/Ag-Patches Antibody (from Patient Serum) Complex Formation Tendency
3.3.1 Dot Blot and ELISA-Based Validation of Epitopes, Ag-Patches, MEVs, and MPVs
3.4 Multi-epitope Vaccine and Multi-patch Vaccine Design
3.5 In Silico Characterization of CTL and HTL Multi-epitope Vaccines
3.5.1 Interferon Gamma-Inducing Epitopes Prediction from Designed MEVs
3.5.2 MEVs and MPVs Allergenicity and Antigenicity Prediction and Physicochemical Analysis
3.5.3 In Silico Tertiary Structure Modeling, Refinement, and Validation of MEVs and MPVs
3.5.4 Discontinuous B Cell Epitope Prediction from MEVs and MPVs
3.5.5 Molecular Interaction Analysis of MEV and MPV with Immunological Receptor
3.5.6 Analysis of cDNA of MEV and MPV for Cloning and Expression in Human Cell Lines
3.6 Preparation of the MEV and MPV Constructs
3.6.1 Expression and Purification of the MEV and MPV Constructs
3.6.2 Complex Formation Tendency of MEV/MPV with Serum Antibodies from Coronavirus Patient and from Experimental Animal Model
4 Notes
Declaration: Patents filed: IN202011037585, IN202011037939, PCT/IN2021/050841.References
Chapter 8: Use of Micro-Computed Tomography to Visualize and Quantify COVID-19 Vaccine Efficiency in Free-Breathing Hamsters
1 Introduction
2 Materials
2.1 SARS-CoV-2 Strain
2.2 Cell Culture and Media
2.3 Vaccine
2.4 Animals
2.5 Micro-Computed Tomography (μCT)
2.6 Anesthesia
2.7 Network Connection and Data Storage
2.8 Software
2.9 Experimental Endpoint
3 Methods
3.1 Immunization of Hamsters
3.2 Experimental SARS-CoV-2 Infection
3.3 μCT Acquisition
3.3.1 Skyscan 1278
3.3.2 X-Cube
3.4 μCT Scan Reconstruction
3.4.1 Skyscan 1278
3.4.2 X-Cube
3.5 Micro-CT Data Visualization
3.6 Micro-CT Data Quantification
3.6.1 Semiquantitative Scoring of Visual Observations in Micro-CT Data
3.6.2 Quantification of μCT-Derived Biomarkers
3.7 Experiment Termination, Endpoint, and Validation
4 Notes
References
Chapter 9: Design of Replication-Competent VSV- and Ervebo-Vectored Vaccines Against SARS-CoV-2
1 Introduction
2 Materials
2.1 Cloning
2.2 Virus Rescue
2.3 TCID50 Assay to Determine Live Virus Titers
2.4 Growth of Recombinant VSV and Purification
3 Methods
3.1 Cloning
3.2 Transfection and Rescue
3.3 TCID50 Assay to Determine Virus Titers
3.4 Stock Virus Production and Purification
4 Notes
References
Chapter 10: CRISPR Engineering of Bacteriophage T4 to Design Vaccines Against SARS-CoV-2 and Emerging Pathogens
1 Introduction
2 Materials
2.1 Plasmid Construction
2.2 Recombinant Phage Construction
2.3 Phage Production and Purification
3 Methods
3.1 Construction of CRISPR-Cas12a Spacers Targeting Hoc or Soc
3.2 Construction of Ee-Hoc and Soc-RBD Donors
3.2.1 Ee-Hoc Donor Construction
3.2.2 Soc-RBD Donor Construction
3.3 Transformation of Spacer and Donor into E. coli
3.3.1 Making B40 Competent Cells
Day 1
Day 2
Day 3
3.3.2 Spacer Plasmid Transformation into B40
3.3.3 Making B40-Spacer Competent Cells
3.3.4 Donor Plasmid Transformation into B40-Spacer Cells
3.4 Construction of T4-Soc-RBD and T4-Ee-Hoc Recombinant Phages by CRISPR Engineering
3.4.1 Measuring Efficiency of Plating (EOP)
3.4.2 Recombinant Phages Construction
3.5 Recombinant Phage Purification for Immunization
3.5.1 Preparation of Phage Working Stock from “Zero Stock´´
3.5.2 Phage Production
3.5.3 Phage Purification
4 Notes
References
Chapter 11: Techniques for Developing and Assessing Immune Responses Induced by Synthetic DNA Vaccines for Emerging Infectious…
1 Introduction
1.1 Challenge
1.2 Vaccine and Immunization Assessment
1.3 Development of Antigen-Specific Synthetic DNA Vaccines Against Emerging Infectious Diseases
1.4 Design of Synthetic DNA Vaccines
1.5 Immune Focusing Using Domain Minimization and Glycan Resurfacing
1.6 Design of Next-Generation DNA-Launched Nanoparticle Vaccines
2 Methods
2.1 Western Blot (or Immunoblot) Analysis
2.1.1 Materials
2.1.2 Preparation of Lysate
2.1.3 Sample Preparation
2.1.4 Preparation, Loading, and Running of the Gel
2.1.5 Transfer of Proteins to Membrane and Blocking
2.1.6 Staining with Primary and Secondary Antibody
2.2 Immunofluorescence Assay
2.2.1 Materials
2.2.2 Sample Preparation
2.2.3 Immunostaining
2.3 Biophysical and Antigenic Profile Characterization of Produced Antigens
3 Animal and Ethics
4 Ex Vivo Immune Assays for Measuring Vaccine-Specific Immune Responses
4.1 Enzyme-Linked Immunosorbent Assay
4.1.1 Reagent Preparation
4.1.2 Antigen Coating
4.1.3 Measurement of Antibody Binding
4.2 Enzyme-Linked Immunospot (ELISpot) Assay for IFN-γ Measurements
4.2.1 Buffers and Reagents
4.2.2 Preparation and Blocking of Plate (Sterile Conditions): Day 1
4.2.3 Incubation of Cells in Plate (Sterile Conditions): Day 2
4.2.4 Detection of Spots: Day 3
4.3 Measurements of Vaccines-Specific Cytokines Production for T Cell Immunity by FACS Analysis
4.3.1 Material Preparations
4.3.2 Cell Preparation for FACS Analysis
4.3.3 Extracellular and Intracellular Staining
5 Neutralization Techniques
5.1 Live Virus Neutralization Assays
5.2 Plaque Reduction Neutralization Test (PRNT) Assay
5.3 Antiviral-Based Cytopathic Effect Assay (CPE assay)
5.4 Neutralization Assay with Pseudotyped Virus
5.4.1 Materials to Produce Pseudovirus
6 Antibody Glycosylation to Measure Humoral Response
6.1 IgG N-glycan Analysis by Capillary Gel Electrophoresis
6.1.1 Materials
6.1.2 Deglycosylation and Labeling of Free N-glycans
6.1.3 Clean Up the Labeled N-glycans
6.1.4 N-glycans Profiling
7 Protective Efficacy Assessment for Vaccine
8 Summary
References
Chapter 12: Towards Determining the Epitopes of the Structural Proteins of SARS-CoV-2
1 Introduction
2 Materials
2.1 Bioinformatics
2.2 Animals and Immunization
2.3 Reagents and Plasticwares
2.4 Software
3 Methods
4 Notes
References
Chapter 13: Development, Production, and Characterization of Hepatitis B Subviral Envelope Particles as a Third-Generation Vac…
1 Introduction
2 Materials
2.1 Lentiviral Production
2.2 Recombinant Mammalian Cell Line Development
2.3 Cell Line Characterization
2.3.1 Flow cytometry
2.3.2 Fluorescence Microscopy
2.4 HBV-SVPs Preparation and Concentration
2.5 HBV-SVPs Characterization
2.5.1 ELISA Analysis
2.5.2 Western Blot Analysis
2.5.3 Transmission Electron Microscopy and Immunogold Analysis
2.6 HBV-SVPs Immunization Protocol
2.6.1 Humoral Immune Response Analysis
2.6.2 Functional Characterization of Antibodies
3 Methods
3.1 Lentivirus Production and Titration
3.2 CHO-K1 Recombinant Cell Line Development
3.3 Cell Line Characterization
3.3.1 Flow Cytometry
3.3.2 Fluorescence Microscopy
3.4 Preparation and Concentration of HBV-SVPs
3.5 Characterization of the HBV-SVPs
3.5.1 ELISA for HBV-VSPs Characterization
3.5.2 Western Blot
3.5.3 Transmission Electron Microscopy and Immunogold Analysis
3.6 Analysis of the Immune Response Triggered by HBV-SVPs
3.6.1 Immunization Protocol
3.6.2 Determination of Total S-Specific Antibody Endpoint Titers
3.6.3 Functional Characterization of Antibodies
4 Notes
References
Chapter 14: Generation of CpG-Recoded Zika Virus Vaccine Candidates
1 Introduction
2 Materials
2.1 Software
2.2 Infectious Subgenomic Amplicons (ISA) Transfection and ZIKV Stock Generation
2.3 Virus Stock Titration
3 Methods
3.1 Design and Generation of Overlapping DNA Fragments
3.2 Infectious Subgenomic Amplicons to Recover Wild-Type and CpG-Recoded ZIKV Variants
3.3 Generation of Wild-Type and CpG-Recoded ZIKV Stocks
3.4 Titration of CpG-Recoded ZIKV Stocks
4 Notes
References
Part IV: Vaccines for Human Bacterial Diseases
Chapter 15: Salmonella Uptake into Gut-Associated Lymphoid Tissues: Implications for Targeted Mucosal Vaccine Design and Deliv…
1 Introduction
2 Materials
2.1 Quantifying Peyer´s Patch Invasion
2.2 Quantification of Colonization by Fecal Shedding
2.3 Isolation and Immunohistochemistry of Intestinal Samples Containing S. Typhimurium
3 Methods
3.1 Quantifying Peyer´s Patch Invasion
3.1.1 Preparation of Bacteria
3.1.2 Gavage
3.1.3 Collection and Processing of Peyer´s Patches
3.1.4 Count Colonies and Compute Competitive Indices (CIs)
3.2 Quantification of Colonization by Fecal Shedding
3.2.1 Preparation of Bacteria
3.2.2 Collection of Fecal Pellets
3.2.3 Processing of Fecal Pellets
3.2.4 Count Colonies and Compute Competitive Indices (CIs)
3.3 Isolation and Immunohistochemistry of Intestinal Samples Containing S. Typhimurium
3.3.1 Preparation of Bacteria and Gavage
3.3.2 Collection of Digestive Tract (Stomach, Small Intestine, Cecum, Large Intestine)
3.3.3 IHC: Deparaffinization and Tissue Rehydration
3.3.4 IHC: Antigen Retrieval (Proteinase K Method)
3.3.5 IHC: Blocking (Rodent Block M and BLOXALL)
3.3.6 IHC: Primary Antibody Application
3.3.7 IHC: AP-Polymer and Chromogen Application
3.3.8 IHC: Counterstain
3.3.9 IHC: Dehydrate Tissue and Apply Coverslips
4 Notes
References
Chapter 16: Development of Human Recombinant Leptospirosis Vaccines
1 Introduction
2 Materials
2.1 Antigen Selection
2.2 Design of Recombinant Constructions
2.3 Cloning of Leptospira Coding Sequences
2.4 Expression of Recombinant Proteins and Solubility Testing
2.5 Solubilization, Purification, and Concentration of Recombinant Proteins
2.6 Immunoblotting Components
2.7 Vaccine Formulation
2.8 Adsorption Test
2.9 Animals
2.10 Blood Collections
2.11 Immunization
2.12 Humoral Immune Response (Indirect ELISA)
2.13 Leptospira sp. Culture and Challenge
2.14 Tissue Collection
3 Methods
3.1 Antigen Selection
3.2 Design and Recombinant Constructions
3.3 Cloning of Native Coding Sequences of Leptospira
3.4 Recombinant Protein Production
3.5 Vaccine Preparation
3.6 Hamster Manipulation
3.7 Blood Collections
3.8 Immunization
3.9 Humoral Immune Response Analyses
3.10 Leptospira sp. Culture and Challenge
3.11 Tissue Collection
3.11.1 Evaluation of Kidney Colonization by Culture
3.11.2 Evaluation of Kidney Colonization by qPCR
4 Notes
References
Chapter 17: Induction of T Cell Responses by Vaccination of a Streptococcus pneumoniae Whole-Cell Vaccine
1 Introduction
1.1 Subtypes and Functions of T Cells
1.2 T Cell Induction by Infection of Bacteria and Virus
1.3 T Cell Induction by Vaccination
1.4 T Cells Induced by Whole-Cell Vaccine
2 Materials
2.1 Strain Selection
2.2 Culture Medium Preparation
2.3 Prepare Bacteria Culture
2.4 Inactivation of Pneumococcal Whole Cell
2.5 Immunize Animals by Intranasal Route
2.6 Immunize Animals by Subcutaneous Route
2.7 Detection of T Cell Responses
2.8 In Vitro Stimulation of Splenocytes
3 Methods
3.1 Prepare Bacteria Culture
3.2 Inactivation of Pneumococcal Whole Cell
3.3 Immunize Animals by Intranasal Route
3.4 Immunize Animals by Subcutaneous Route
3.5 Detection of T Cell Responses
3.6 In Vitro Stimulation of Splenocytes
4 Notes
References
Chapter 18: Development of a Bacterial Nanoparticle Vaccine Against Escherichia coli
1 Introduction
2 Materials
2.1 Bacterial Growth and Antigen Extraction
2.2 Protein and Lipopolysaccharide Content Determination
2.3 SDS Polyacrylamide Gel Components
2.4 Immunoblotting Components
2.5 Nanoparticle Formulation Preparation
2.6 Nanoparticle Characterization
2.7 Nanoparticle Loading Capacity
2.8 Determination of Antigen Integrity
3 Methods
3.1 Bacterial Strain and Growth Conditions
3.2 Antigenic Complex (HT Membrane Vesicles)
3.3 Characterization of the Antigenic Extracts
3.4 Preparation of HT-Loaded Nanoparticles
3.5 Nanoparticle Characterization
3.6 Nanoparticle Loading Capacity
3.7 Determination of Antigen Integrity
4 Notes
References
Chapter 19: Construction of Novel Live Genetically Modified BCG Vaccine Candidates Using Recombineering Tools
1 Introduction
2 Materials
2.1 Chromosomal DNA Preparation
2.2 Plasmid Construction for Recombination Substrate
2.3 Preparation of Recombineering Substrates
2.4 Preparation of Recombinogenic/Electrocompetent BCG
2.5 Electroporation of Recombineering Substrates
2.6 Growth, Verification of Allelic Replacement Mutants, and Recombineering Plasmid Curation
3 Methods
3.1 Chromosomal DNA Preparation
3.2 Plasmid Construction to Produce the Recombination Substrate
3.3 Preparation of Recombinogenic/Electrocompetent Slow Growing Mycobacteria
3.4 Electroporation of the Substrates for Homologous Recombination
3.5 Growth, Verification of Double Homologous Recombination Events, and Curation of the Recombineering Plasmid
4 Notes
References

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