Applications of Advanced Omics Technologies: From Genes to Metabolites - 1st Edition - ISBN: 9780444626509, 9780444626691

Applications of Advanced Omics Technologies: From Genes to Metabolites, Volume 64

1st Edition

Series Volume Editors: Virginia García-Cañas Alejandro Cifuentes Carolina Simó
Hardcover ISBN: 9780444626509
eBook ISBN: 9780444626691
Imprint: Elsevier
Published Date: 4th June 2014
Page Count: 496
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Table of Contents

  • 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

Description

  • 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

Key Features

  • Describes the latest applications of omics technologies
  • Provides an excellent reference for applications of advanced omics techniques
  • Includes advanced tools and methodologies for dealing with the data generated

Readership

Analytical scientists, PhD students and technicians in control laboratories, universities, hospitals, research laboratories and regulation agencies


Details

No. of pages:
496
Language:
English
Copyright:
© Elsevier 2014
Published:
Imprint:
Elsevier
eBook ISBN:
9780444626691
Hardcover ISBN:
9780444626509

About the Series Volume Editors

Virginia García-Cañas Series Volume Editor

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 Series Volume Editor

Dr. Alejandro Cifuentes is a Full Research Professor at the National Research Council of Spain (CSIC) in Madrid and Head of the Laboratory of Foodomics. He has been Director of the Institute of Food Science Research and Deputy Director of the Institute of Industrial Fermentations, both belonging to CSIC. Currently he is Director of the Metabolomics Platform belonging to the International Excellence Campus UAM+CSIC. Alejandro's activity includes the development of advanced analytical methods (e.g., metabolomics, transcriptomics, proteomics) for foodomics, food quality and safety, as well as extraction and characterization of bioactive compounds from natural sources and their effect on human health. He holds different national and international awards, is member of the Editorial Board of 11 international journals (including J. Chromatogr. A, J. Pharmaceut. Biomed., J. Sep. Sci., Food Anal. Method., Int. J. Mol. Sci.) and Editor of TrAC-Trends in Analytical Chemistry, Electrophoresis and Current Opinion in Food Science (Foodomics Section). He has published more than 230 SCI papers, 20 books and book chapters and 8 patents. His h index is 56 (February 2016) and his works have received more than 10000 citations. Alejandro has given more than 150 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 Series Volume Editor

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