Packed with methods and techniques, this book presents a standard operating procedure for sample selection, preparation, and storage, as well as data analysis and modeling. Authoritative and practical, from protein sequence to function will appeal to students in biochemistry, molecular biology and genetics and all postgraduates and researchers with an interest in genomics and proteomics.
Author(s): Mohamed A. Selmy
Publisher: Delve Publishing
Year: 2018
Language: English
Pages: 300
City: Oakville
Cover
Half Title Page
Title Page
Copyright Page
About The Author
Table of Contents
List of Figures
List of Tables
List of Abbreviations
Preface
Chapter 1 Biomarkers: An Overview
1.1. Introduction
1.2. Classification of Biomarkers
1.3. Types of Biomarkers Based on Different “Omics"
1.4. Biomarker Specifications
1.5. An Overview of Biomarkers In A Clinical Scenario
1.6. Characters of Ideal Biomarkers
1.7. Biomarkers or Clinical Endpoints
1.8. Merits And Demerits of Biomarkers As Surrogate Endpoints
1.9. Which Are The Biomarkers Used?
1.10. Gist of Significance of Biomarkers
1.11. Case Studies of Analysis of Biomarkers In A Clinical Context
1.12. Discovery and Validation of Biomarkers
1.13. Biomarkers In A Clinical Scenario: Approach
1.14. Valid Biomarkers and Clinical Research
1.15. Case Study of Biomarkers Detected By Metabolomics
1.16. Summary
References
Chapter 2 Proteomics: An Overview of Techniques Involved
2.1. Design of Biomarkers
2.2. Biobanking of Samples
2.3. Proteomics And Discovery of Biomarkers
2.4. A Quick Snapshot
2.5. Techniques For Biomarker Discovery Using Proteomics
2.6. The Mass Analyzers
2.7. Variations of Ms
2.8. Variations In Ms Technologies In Proteomics
2.9. Ief Fractionation Methods
2.10. 2D Gel Electrophoresis (2-De)
2.11. 2D Difference Gel Electrophoresis (2D-Dige)
2.12. Stable Isotope Labeling by Amino Acids In Cell Culture (SILAC)
2.13. Isotope-Coded Affinity Tag (ICAT)
2.14. Western Blotting
2.15. 18O Stable Isotope Labeling
2.16. Isobaric Tagging Reagent For Absolute Quantitation (ITRAQ)
2.17. Ce-Ms
2.18. Stable Isotope Dilution Mass Spectrometry (SID-MS)
2.19. Microarrays
2.20. Multidimensional Protein Identification Technology (MUDPIT)
2.21. Label-Free Techniques
2.22. Another Proteomics For Biomarker Discovery
2.23. Bioinformatics and Proteomics And Biomarkers
2.24. Glimpses of Discovery of Biomarkers Using Proteomics
2.25. Case Studies: Biomarkers of Bladder Cancer Using Proteomics
2.26. Final Note
References
Chapter 3 Microbial Biomarkers Proteomics
3.1. Typing Of Microbes
3.2. Typing Methods
3.3. Phenotypic Methods
3.4. Genotypic Methods
3.5. Diagnosis Of Microbial Infections Using Biomarkers
3.6. What Is The Role Of A Biomarker From The Host?
3.7. Biomarkers And Antibiotics: A Scenario
3.8. Biomarkers That Are Routinely Analyzed
3.9. Biomarkers For The Future
3.10. What’s New?
3.11. Proteome For Biomarkers Of Bacteria And Virus
3.12. Host–Pathogen Protein–Protein Interactions
3.13. Intact Proteins
3.14. Direct Interactions And Their Detections
3.15. Posttranslational Modifications That Are Regulated By Pathogen
3.16. Summary
References
Chapter 4 Plant Biomarkers Discovery by Proteomics
4.1. Introduction
4.2. Why Proteomics For Plant Biomarkers?
4.3. Approaches For Plant Biomarkers
4.4. Proteomics For Reactive Oxygen Species Research
4.5. Stress Responses In Two Plants: Proteomics For Biomarkers
4.6. Proteomics For Plants Infected With Virus: Biomarkers
4.7. The Advantages of Proteomics
4.8. Protein Microarrays For Biomarkers
4.9. Other Approaches
4.10. Interpreting The Data Using Bioinformatics
4.11. Proteomics For Food From Agriculture: Biomarkers:
4.12. Biomarkers For Biofuels
4.13. Biomarkers For Important Crops: Applications of Proteomics
4.14. Proteomics of Plants For Biomarkers: An Organ Wise Approach
4.15. Biomarkers: Proteomic Analysis of Seedlings of Crops
4.16. Proteomics And Biomarkers
4.17. Root Proteomics
4.18. Leaf Proteomics
4.19. Xylem And Phloem Proteomics
4.20. Summary
References
Chapter 5 Biomarkers For Animals by Proteomics
5.1. Introduction
5.2. Health of Farm Animals: Biomarkers
5.3. Proteomics And Veterinary Research
5.4. Proteomics Techniques For Animal Biomarker Discovery
5.5. Sample Preparation
5.6. Points to be Considered in the Terms of Animal Biomarkers
5.7. Veterinary Research and Biomarkers
5.8. Pathogen Proteomics
5.9. Avian Proteomics
5.10. Proteomics In Aquaculture
5.11. Parasite Proteomics
5.12. Animal Proteomics in Different Tissues
5.13. Overview of Serum Proteomics in Farm Animals
5.14. Biomarkers Using Proteomics of Animal Products
5.15. Case Study of Biomarkers: Targeting The Mosquito
5.16. Scenario/Future For Animal Proteomics
5.17. Summary
References
Chapter 6 Clinical Biomarkers And Proteomics
6.1. Introduction
6.2. Overview of Biomarkers
6.3. Historical Background
6.4. Role of Biomarkers In Drug Development
6.5. Brief Regulatory Aspects
6.6. Utility of Biomarkers In Clinical Studies
6.7. Biomarkers In Clinical Evaluation
6.8. Urine Biomarkers
6.9. Serum Biomarkers
6.10. Classes of Biomarkers
6.11. Efficacy Biomarkers
6.12. Surrogate Biomarkers
6.13. Predictive Biomarkers
6.14. Pharmacodynamic (PD) Biomarkers
6.15. Prognostic Biomarkers
6.16. Discrepant Results And Its Major Impact on Clinical Trials
6.17. Lack of Traceability as a Major Source of Systematic Errors
6.18. Impact of Discrepant Results on Personalized Medicine
6.19. Mass Spectrometry And Marker Detection
6.20. Conclusion
References
Chapter 7 Biomarkers of Cancer Using Proteomics
7.1. Discovery of Biomarkers of Cancer
7.2. Types of Biomarkers
7.3. Diagnosis of Cancer By Using Proteomics
7.4. Proteomics Approaches Towards The Early Detection And Diagnosis of Cancer
7.5. Proteomic Techniques In Cancer
7.6. Clinical Utility
7.7. Clinical And Analytical Necessities For Biomarker Presentation
7.8. Proteomic Approach In Different Types of Cancer
7.9. Challenges
7.10. Perspectives For Proteomics In Cancer
7.11. Summary
References
Chapter 8 Future Directions, Challenges and Solutions
8.1. Introduction
8.2. Challenges In Biomarkers For Proteomics
8.3. Proteomics vs. Genomics
8.4. Overcoming Challenges in Data Interpretation
8.5. Future Expectations
8.6. Points For Consideration
References
Index
