Front Cover

Applications of Advanced Omics Technologies: From Genes to Metabolites

Copyright

Dedication

Contents

Contributors to Volume 64

Series Editor´s Preface

Preface

Part I: Genomics and Transcriptomics

Chapter 1: Applications of Functional Gene Microarrays for Profiling Microbial Communities

1. Introduction

2. Comparison of Microarrays with High-Throughput Sequencing

3. Functional Gene Arrays

3.1. GeoChip Microarrays

3.2. Other FGAs

3.2.1. Hydrogenase Chip

3.2.2. Food Safety and Health Applications

3.2.3. Detection of Novel Sequences

3.2.4. Other Microarrays: Unique Applications

4. Key Issues in Microarray Application

5. Future Advancements

6. Conclusions

Acknowledgments

References

Chapter 2: microRNA Profiling: An Overview of Current Technologies and Applications

1. Introduction

2. miRNA Biogenesis and Nomenclature

3. Considerations for miRNA Profiling

4. miRNA Extraction

5. qPCR Analysis of miRNAs

6. Microarray Profiling of miRNAs

7. Small RNA-seq

8. In Silico miRNA Analysis Resources

9. miRNA Functional Analysis

10. Recent Developments in the Application of miRNA Profiling to Cancer Research

11. Conclusions

References

Chapter 3: Application of Novel Genotyping Microarray Technologies in Cancer Research

1. Introduction

2. Cancer Genetics: From Biology to Clinical Practice

2.1. The Discovery of Cancer Genetics

2.2. The Introduction of Cancer Genetics on Cancer Therapy

2.3. Tumor Genome Analysis Applied to Improve Cancer Therapy

3. Genotyping Technologies

3.1. The Study of Defined Variants at the Level of DNA

3.1.1. Variants Discovery by Sequencing

3.1.2. Alternative Techniques for the Analysis of Defined Variants

3.1.3. Real-Time PCR-Based Techniques

3.1.4. Whole-Genome SNP Analysis

3.2. Analysis of DNA Variation Independent from Single Nucleotide Polymorphisms

3.3. Variants Found in Small Numbers

3.4. Gene Expression Studies

4. Next-Generation Genomic Techniques

5. Applications of Novel SNP Technologies in Cancer Research

6. Conclusions and Future Directions

References

Chapter 4: Applications of Next-Generation Sequencing Technologies to the Study of the Human Microbiome

1. Introduction

1.1. 16S Sequencing Technologies

2. Next-Generation Sequencing

2.1. Roche 454 Pyrosequencing

2.1.1. Barcoding

2.1.2. Sequencing Parameters

2.2. Illumina SBS Platform (Genome Analyzer IIx, HiSeq, MiSeq)

2.3. AB (Applied Biosystems) SOLiD Platform (AB 5500, 5500xl)

2.4. Pacific Bioscience SMRT Platform (PacBio RS II)

2.5. Ion Torrent (PostLightTM) Semiconductor Platform (Ion PGM, Ion Proton)

3. Bioinformatics

3.1. Denoising

3.2. Detecting Chimeras

3.3. Operational Taxonomic Units

3.4. Sequence Alignment

3.5. Phylogenetic Analysis

3.6. Estimating Diversity

3.7. Comparing Between Communities

3.8. Unifying Platforms

4. The Microbiome in Health and Disease

4.1. The Gastric Microbiome

4.2. The Colonic Microbiota and Colorectal Cancer

4.3. The Colonic Microbiota and Inflammatory Bowel Disease

4.4. Irritable Bowel Syndrome

4.5. The Gut Microbiota and Diseases of the Liver

4.6. Host Diet, Metabolism, and the Gut Microbiota

4.6.1. The Gut Microbiome and Obesity

4.6.2. The Gut Microbiome and Type II Diabetes

4.6.3. The Gut Microbiome and Cardiovascular Disease

4.7. The Gut Microbiome and Renal Physiology

4.8. The Gut Microbiota and Rheumatoid Arthritis

4.9. The Cutaneous Microbiome

4.10. Emerging Research Involving the Lung Microbiome

References

Chapter 5: Emerging RNA-Seq Applications in Food Science

1. Introduction

2. Overview of RNA-Seq Technology

2.1. Library Preparation and Clonal Amplification

2.2. Sequencing Chemistry

2.3. Data Analysis

3. Applications of RNA-Seq

3.1. De Novo Transcriptome Assembly

3.2. Comparative Transcriptomic Analysis/Digital Gene-Expression Profiling

3.3. Splicing Analysis

3.4. MicroRNA-Seq

4. RNA-Seq in Food Science

4.1. Production of Food Crops

4.2. Foodborne Pathogenic Microorganisms

4.3. Food Fermentations

5. Future Outlooks and Conclusions

Acknowledgments

References

Part II: Proteomics and Peptidomics

Chapter 6: Making Progress in Plant Proteomics for Improved Food Safety

1. Introduction

2. Current Technologies in Plant Proteomics Sample Treatment

3. The Power of Hexapeptide Ligand Libraries

4. Examples of Plant Proteomics Studies Focusing on Low-Abundance Species

4.1. Plants as Basis for Food

4.2. Plants as Basis for Drinks

5. Proteomics Applications in Food Security

6. The Innovative Involvement of CPLL in Plant Allergen Discovery

7. Toward Possible New Steps

References

Chapter 7: Advantages and Applications of Gel-Free Proteomic Approaches in the Study of Prokaryotes

1. Introduction

1.1. Proteomics and Integration with Genomics and Transcriptomics

1.2. Accessibility of Quantitative Proteomics

1.3. Gel-Based Proteomics

2. Proteomic Workflows

2.1. Protein Extraction and Immediate Postanalysis

2.2. Use of Surfactants

2.3. Subproteome Analysis via Shaving

2.4. Moonlighting Proteins

2.5. Proteome Stability

2.6. Fractionation on Gels or Columns

3. Affinity Chromatography Applications

3.1. Enrichment of the Phosphoproteome

3.2. Glycoproteomics

3.3. Membrane Protein Tagging

3.4. Immunodepletion of Highly Abundant Proteins

3.5. Interactome Analysis

3.6. Combinatorial Libraries

3.7. Lab-on-a-Chip Applications

4. Gel-Free Peptide Chromatography and Mass Spectrometry

4.1. Protein Digestion

4.2. Liquid Chromatography of Peptides

4.3. Mass Spectrometers for Gel-Free Proteomics

5. Labeling and Label-Free Approaches for Protein Quantification

5.1. Spectral Counting

5.2. MS1 Features and Quantification

5.3. Stable Isotope Labeling with Amino Acids

5.4. Isotope-Coded Affinity and Covalent Tagging Methods

5.5. Metabolic Labeling

6. Peptide Identification

6.1. Data-Dependent Acquisition

6.2. Data-Independent Acquisition

7. Proteomic Data Postanalysis

7.1. Bioinformatic Pipelines

7.2. Statistical Treatment of Quantitative Proteomic Data

7.3. Functional Profiling and Data Visualization Using Proteomic Data

7.4. Metabolic Modeling and Proteomics

8. State of Affairs in the Study of Prokaryotes via Gel-Free Proteomics

9. Conclusions and Future Prospects

Acknowledgments

References

Chapter 8: Proteomics Tools for Food Fingerprints: Addressing New Food Quality and Authenticity Challenges

1. Introduction

2. Proteomics

2.1. Discovery Phase

2.2. Target-Driven Phase

3. Proteomics for Addressing New Food Quality and Authenticity Challenges

3.1. Food Authentication

3.2. Allergen Detection

3.3. Monitoring of Food Spoilage or Pathogenic Microbes

3.4. Monitoring of Changes of Food Quality During the Storage and Processing

4. Innovative Protein-Based Technologies

5. Concluding Remarks and Future Directions

References

Chapter 9: Salivary Peptidomics Targeting Clinical Applications

1. Introduction

2. Sample Preparation for Salivary Peptidome

3. Methodologies for Salivary Peptidome Analysis

4. Functional Relevance of Salivary Peptidome

5. The Missing Link: Connecting Peptides to Peptidases

6. Impact of Diseases in the Human Salivary Peptidome

7. Future Perspective

Acknowledgments

References

Part III: Metabolomics

Chapter 10: Metabolomics in the Study of Alzheimer's Disease

1. Introduction

2. Metabolomics in AD

2.1. Metabolomics and AD in CSF

2.2. Metabolomics and AD in Plasma and Serum

2.3. Metabolomics and AD in Postmortem BT

3. Conclusions and Future Research

Acknowledgments

References

Chapter 11: Application of Metabolomics to Cardiovascular and Renal Disease Biomarker Discovery

1. Introduction

1.1. Cardiorenal Syndrome

1.2. CV Risk and On-Time Action: The Real Challenge

2. What to Expect from the ``Omics´´: Changing the Perspective

3. Metabolomics in CVD

3.1. Metabolic Fingerprinting in CVD

3.2. Metabolic Profiling in CVD

3.3. Metabolomics Directly in Tissue

4. Metabolomics in Renal Disease

5. Approaching the Cardiorenal Puzzle

6. Microvesicles: A Novel Source of Biomarkers

6.1. Metabolomics in Exosomes Research

6.2. Metabolomics in MP Research

References

Chapter 12: The Clinical Application of Proteomics and Metabolomics in Neonatal Medicine

1. Introduction

2. A Brief History of Newborn Screening

2.1. The Role of Clinical MS

2.2. The Dried Blood Spot

2.3. MS: Selectivity

2.4. MS: Isotope Dilution

2.5. Interpretation of Results

2.6. MS/MS Validation

3. Clinical Correlates: What the Physician Needs to Know at the Bedside

4. Beyond Newborn Screening: Additional Clinical Applications and the Potential for the Future

4.1. Nutritional Effects on Neonatal Metabolism

4.2. Future Applications: Integrated Clinical Proteomic/Metabolomic Screening

5. Initial Emerging Avenues for Fetal and Neonatal Assessment with Proteomics and Metabolomics

5.1. Fetal Evaluation

5.2. Neonatal Evaluation

5.3. Nutritional Considerations

5.4. Other Avenues for Neonatal Critical Care Monitoring with Tandem Mass Spectroscopy

5.5. Neonatal Septicemia

5.6. Hypoxic-Ischemic Brain Injury, Perinatal Asphyxia, and Chronic Lung Disease: The Potential for Proteomic Evaluation

6. Tailored Drug Therapy for the Neonate

7. Summary

References

Part IV: Other Omics Strategies, Data Treatment, Integration and Systems Biology

Chapter 13: Profiling of Genetically Modified Organisms Using Omics Technologies

1. Introduction

2. Debated Safety Issues on GMOs

3. Omics Profiling in GMO Analysis

3.1. Transcriptomics

3.2. Proteomics

3.3. Metabolomics

3.3.1. Nuclear Magnetic Resonance

3.3.2. MS-Based Technologies

3.3.3. Multi-platform Strategies

3.4. Cross-Omics Studies

4. Future Outlook and Conclusions

Acknowledgments

References

Chapter 14: MS-Based Lipidomics

1. Introduction

2. Sample Preparation

3. Lipid Analysis

3.1. Shotgun Lipidomics

3.2. LC-MS

3.3. Surface Analysis of Lipids

4. Identification

5. Data Processing for MS-Based Lipidomics

6. Conclusions

References

Chapter 15: Foodomics: Food Science and Nutrition in the Postgenomic Era

1. Introduction to Foodomics

2. Omics Tools Used in Foodomics

2.1. Transcriptomics

2.1.1. Gene Expression Microarray Technology

2.1.2. Sequencing-Based Technologies

2.2. Proteomics

2.2.1. Bottom-Up Approach

2.2.2. Top-Down Approach

2.2.3. Other Proteomic Approaches

2.3. Metabolomics

2.3.1. Mass Spectrometry Approaches for Metabolomics

2.3.2. Nuclear Magnetic Resonance Approaches for Metabolomics

2.4. Other Omic Approaches

2.4.1. Mirnomics

2.4.2. Epigenomics

2.4.3. Peptidomics

2.4.4. Lipidomics

2.4.5. Glycomics

3. Data Analysis and Integration: Foodomics and Systems Biology

4. Present Applications of Foodomics

4.1. Foodomics in Food Safety, Quality, and Traceability Studies

4.2. Foodomics of Transgenic Foods

4.3. Foodomics in Nutrition and Health Research

4.3.1. Foodomics, Functional Foods, and Nutraceuticals

4.3.2. Foodomics and the Human Gut Microbiome

4.4. Green Foodomics

5. Future Trends and Opportunities for Foodomics

5.1. Foodomics and Personalized Nutrition: How Far We Are?

5.2. The Role of Foodomics in Pangenomics

Acknowledgments

References

Chapter 16: Omics Data Integration in Systems Biology: Methods and Applications

1. Introduction

2. Integrated Database Resources

3. Integrative Omics Analysis

3.1. Meta-Analysis

3.2. Multivariate Analysis

3.3. Gene Regulatory Networks

3.4. Integrating Genome Variation Data

4. Tools for Integrative Visualization of Omics Data

5. Conclusions and Future Prospects

Acknowledgments

References

Index