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Applications of Advanced Omics Technologies: From Genes to Metabolites

1st Edition - May 8, 2014

Editors: Virginia García-Cañas, Alejandro Cifuentes, Carolina Simó

Hardback ISBN:

9 7 8 - 0 - 4 4 4 - 6 2 6 5 0 - 9

eBook ISBN:

9 7 8 - 0 - 4 4 4 - 6 2 6 6 9 - 1

The book contains contributions concerning the application of the new instrumental and methodological developments in omics technologies, including those related to Genomics,… Read more

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The book contains contributions concerning the application of the new instrumental and methodological developments in omics technologies, including those related to Genomics, Transcriptomics, Proteomics, Peptidomics and Metabolomics, Lipidomics and Foodomics.The16 chapters discuss in detail: innovative applications of functional gene microarrays for profiling microbial communities, microRNA profiling, novel genotyping applications using microarray technology in cancer research, next-generation sequencing applied to the study of human microbiome, emerging RNA-SEQ applications in food science, recent progress in plant proteomics, applications of gel-free proteomic approaches, the challenges and applications of proteomics tools for food authenticity, the role of salivary peptidomics in clinical applications, metabolomic approaches to the study of degenerative, cardiovascular and renal diseases, and neonatal medicine. Also covered are other omics applications such as profiling of genetically modified organisms, the fundamentals, applications and challenges of foodomics, and MS-based lipidomics. Moreover, this volume includes relevant and updated aspects on bioinformatics, data treatment, data integration and systems biology. This book complements the previous volume "Fundamentals of Advanced Omics Technologies: New Advances from Genes to Metabolites" that covered the fundamental aspects of these new omics technologies.

Dedication
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
  - Abstract
  - 1 Introduction
  - 2 Comparison of Microarrays with High-Throughput Sequencing
  - 3 Functional Gene Arrays
  - 4 Key Issues in Microarray Application
  - 5 Future Advancements
  - 6 Conclusions
  - Acknowledgments
- Chapter 2: microRNA Profiling: An Overview of Current Technologies and Applications
  - Abstract
  - 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
- Chapter 3: Application of Novel Genotyping Microarray Technologies in Cancer Research
  - Abstract
  - 1 Introduction
  - 2 Cancer Genetics: From Biology to Clinical Practice
  - 3 Genotyping Technologies
  - 4 Next-Generation Genomic Techniques
  - 5 Applications of Novel SNP Technologies in Cancer Research
  - 6 Conclusions and Future Directions
- Chapter 4: Applications of Next-Generation Sequencing Technologies to the Study of the Human Microbiome
  - Abstract
  - 1 Introduction
  - 2 Next-Generation Sequencing
  - 3 Bioinformatics
  - 4 The Microbiome in Health and Disease
- Chapter 5: Emerging RNA-Seq Applications in Food Science
  - Abstract
  - 1 Introduction
  - 2 Overview of RNA-Seq Technology
  - 3 Applications of RNA-Seq
  - 4 RNA-Seq in Food Science
  - 5 Future Outlooks and Conclusions
  - Acknowledgments
Part II: Proteomics and Peptidomics
- Chapter 6: Making Progress in Plant Proteomics for Improved Food Safety
  - Abstract
  - 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
  - 5 Proteomics Applications in Food Security
  - 6 The Innovative Involvement of CPLL in Plant Allergen Discovery
  - 7 Toward Possible New Steps
- Chapter 7: Advantages and Applications of Gel-Free Proteomic Approaches in the Study of Prokaryotes
  - Abstract
  - 1 Introduction
  - 2 Proteomic Workflows
  - 3 Affinity Chromatography Applications
  - 4 Gel-Free Peptide Chromatography and Mass Spectrometry
  - 5 Labeling and Label-Free Approaches for Protein Quantification
  - 6 Peptide Identification
  - 7 Proteomic Data Postanalysis
  - 8 State of Affairs in the Study of Prokaryotes via Gel-Free Proteomics
  - 9 Conclusions and Future Prospects
  - Acknowledgments
- Chapter 8: Proteomics Tools for Food Fingerprints: Addressing New Food Quality and Authenticity Challenges
  - Abstract
  - 1 Introduction
  - 2 Proteomics
  - 3 Proteomics for Addressing New Food Quality and Authenticity Challenges
  - 4 Innovative Protein-Based Technologies
  - 5 Concluding Remarks and Future Directions
- Chapter 9: Salivary Peptidomics Targeting Clinical Applications
  - Abstract
  - 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
Part III: Metabolomics
- Chapter 10: Metabolomics in the Study of Alzheimer's Disease
  - Abstract
  - 1 Introduction
  - 2 Metabolomics in AD
  - 3 Conclusions and Future Research
  - Acknowledgments
- Chapter 11: Application of Metabolomics to Cardiovascular and Renal Disease Biomarker Discovery
  - Abstract
  - 1 Introduction
  - 2 What to Expect from the “Omics”: Changing the Perspective
  - 3 Metabolomics in CVD
  - 4 Metabolomics in Renal Disease
  - 5 Approaching the Cardiorenal Puzzle
  - 6 Microvesicles: A Novel Source of Biomarkers
- Chapter 12: The Clinical Application of Proteomics and Metabolomics in Neonatal Medicine
  - Abstract
  - 1 Introduction
  - 2 A Brief History of Newborn Screening
  - 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
  - 5 Initial Emerging Avenues for Fetal and Neonatal Assessment with Proteomics and Metabolomics
  - 6 Tailored Drug Therapy for the Neonate
  - 7 Summary
Part IV: Other Omics Strategies, Data Treatment, Integration and Systems Biology
- Chapter 13: Profiling of Genetically Modified Organisms Using Omics Technologies
  - Abstract
  - 1 Introduction
  - 2 Debated Safety Issues on GMOs
  - 3 Omics Profiling in GMO Analysis
  - 4 Future Outlook and Conclusions
  - Acknowledgments
- Chapter 14: MS-Based Lipidomics
  - Abstract
  - 1 Introduction
  - 2 Sample Preparation
  - 3 Lipid Analysis
  - 4 Identification
  - 5 Data Processing for MS-Based Lipidomics
  - 6 Conclusions
- Chapter 15: Foodomics: Food Science and Nutrition in the Postgenomic Era
  - Abstract
  - 1 Introduction to Foodomics
  - 2 Omics Tools Used in Foodomics
  - 3 Data Analysis and Integration: Foodomics and Systems Biology
  - 4 Present Applications of Foodomics
  - 5 Future Trends and Opportunities for Foodomics
  - Acknowledgments
- Chapter 16: Omics Data Integration in Systems Biology: Methods and Applications
  - Abstract
  - 1 Introduction
  - 2 Integrated Database Resources
  - 3 Integrative Omics Analysis
  - 4 Tools for Integrative Visualization of Omics Data
  - 5 Conclusions and Future Prospects
  - Acknowledgments
Index

Virginia García-Cañas

Virginia García-Cañas works in the Laboratory of Foodomics on the development of advanced analytical methods for: Foodomics, including Genomics and Transcriptomics; food quality; food safety; and Nutrigenomic studies. Her research covers: i) development of advanced DNA/RNA-based methods for food analysis (genetically-modified organisms, pathogens, etc.), and ii) Nutrigenomic study of the effect of dietary polyphenols on cancer. She has published over 45 SCI papers and 7 book chapters. Her h index is 19 and her works have received over 900 citations (August-2013).

Affiliations and expertise

Laboratory of Foodomics, CSIC, Madrid, Spain

Alejandro Cifuentes

Alejandro Cifuentes is a Full Research Professor at the National Research Council of Spain (CSIC) in Madrid, Head of the Laboratory of Foodomics and Director of the Metabolomics Platform (International Excellence Campus CSIC + University Autonoma of Madrid). He has been Founding Director of the Institute of Food Science Research and Deputy Director of the Institute of Industrial Fermentations, both belonging to CSIC. Alejandro's activity includes advanced analytical methods development for Foodomics (including transcriptomics, proteomics and metabolomics), food quality and safety, as well as isolation and characterization of natural bioactive compounds and their effect on human health. He holds different national and international awards, is member of the Editorial Board of 17 international journals (including Journal of Chromatography A, Journal of Separation Science, Food Analytical Methods, International Journal of Molecular Sciences, Heliyon, Journal of Pharmaceutical Analysis, etc.), Editor of TrAC-Trends in Analytical Chemistry and Electrophoresis, and Editor-in-Chief of Open Life Sciences. He has published more than 270 SCI papers, 30 books and book chapters and 9 patents. His h index is 70 (Google scholar, June 2020) and his works have received more than 17000 citations. Alejandro has given more than 200 invited lectures in different national and international meetings in Europe, Asia, Africa, America and Oceania. He has defined for the first time in a SCI journal the new discipline of Foodomics.

Affiliations and expertise

National Research Council of Spain (CSIC), Madrid, Spain

Carolina Simó

Carolina Simó is a Tenured Researcher at the National Research Council of Spain (CSIC) in Madrid, she develops her scientific activities in the Laboratory of Foodomics. Her running research lines include: i) Method development using electrophoretic/chromatographic techniques coupled to mass spectrometry for Proteomics and Metabolomics. ii) Food safety assessment, quality control and other features related to food processing, storage, authenticity; iii) Study of the effect of diet on health/disease and the mechanisms of nutrients and bioactive food components at the molecular level. She has published over 50 SCI papers and 10 book chapters. Her h index is 20 and her works have received over 1000 citations (August-2013).

Affiliations and expertise

Laboratory of Foodomics, CSIC, Madrid, Spain