Concepts and Techniques in OMICS and System Biology
- 1st Edition - August 13, 2024
- Imprint: Academic Press
- Authors: Asmat Farooq, Sajad Majeed Zargar, Parvaze Ahmad Sofi, Jebi Sudan, Uneeb Urwat, Khursheed Hussain
- Language: English
- Paperback ISBN:9 7 8 - 0 - 4 4 3 - 2 1 9 2 3 - 8
- eBook ISBN:9 7 8 - 0 - 4 4 3 - 2 1 9 2 4 - 5
Concepts and Techniques in OMICS and Systems Biology provides a concise and lucid account on the technical aspects of omics, system biology and their application in fields of… Read more
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Request a sales quoteConcepts and Techniques in OMICS and Systems Biology provides a concise and lucid account on the technical aspects of omics, system biology and their application in fields of different life science.
With a strong focus on the fundamental principles understanding of metabolomics, ionomics and system biology, the book also gives an updated account on technical aspects of omics and system biology. Since both omics and systems biology fields are fast advancing filed of biological sciences, its significance and applications need to be understood from the baseline.
In 10 chapters Concepts and Techniques in OMICS and Systems Biology introduces the reader to both Proteomics, Metabolomics and Ionomics, and System Biology, the technical applications, describes both the software in for proteomics as metabolomic enumeration and preludes Omics technologies and their applications.
The chapters are designed in a well-defined chronology such that readers will understand the concepts and techniques involved in omics and system biology. This compilation will be ideal reading material for students, researchers and people working in the industries related to biological sciences.
- Provides an in-depth explanation of fundamental principles regarding the understanding of metabolomics, ionomics and system biology.
- Gives updated account on technical aspects of omics and system biology.
- Includes unique content in its theoretical background, technical approaches and advancements made in omics and systems biology
Master's students in life science subjects like System Biology, Biotechnology, Genetics, Botany, Zoology, Biochemistry, Microbiology and almost all the applied fields of life sciences Researchers in the field of Biotechnology, Genetics, Zoology, Botany and Microbiology. Ph.D. students and postdocs in the concerned field
- Cover image
- Title page
- Table of Contents
- Copyright
- Dedication
- About the authors
- Preface
- Acknowledgments
- Chapter 1. Introduction to proteomics, metabolomics, and ionomics
- Introduction
- Proteomics techniques—Low throughput and high throughput techniques
- Introduction to metabolomics
- Introduction to ionomics
- Applications of proteomics
- Applications of metabolomics
- Application of metabolomics for genetically modified (GM) crops
- Metabolomics and crop improvement
- Applications of ionomics
- Ionomics in normal plant growth
- Ionomics and plant biotic stress
- Ionomics and abiotic stress in crops
- Quantitative trait loci (QTLs) regulating ionomics
- Conclusion
- Chapter 2. Proteomics and the techniques applicable
- Introduction
- Protein primary structure
- Protein secondary structure
- Hydrogen bond
- Psi and phi angles
- Unusual secondary structures
- Motifs
- Tertiary protein structure
- Protein domains
- Quaternary protein structure
- Protein structure determination by X-ray crystallography
- Requirements
- NMR
- Protein structure determination using NMR
- Principles and applications of mass spectrometry
- Principles of Mass spectrometry
- Applications of Mass spectrometry (Pukala & Robinson, 2022)
- Proteomics: Basic understanding
- Conclusion
- Chapter 3. Advances in proteomics techniques
- Introduction
- MASCOT
- pQuant software
- Trans Proteomic Pipeline (TPP) software
- Census software
- MaxQuant software
- Advanced features
- Exploring proteome databases
- UniProt
- NCBI protein
- Ensembl
- Protein Data Bank
- PeptideAtlas
- Human protein Atlas
- PRIDE database
- Human proteome organization proteomics standards initiative repositories
- RefSeq
- SWISS-MODEL repository
- Conclusion
- Chapter 4. Aspects of protein interactions
- Coimmuno precipitation
- Antibody selection
- Cell lysis
- Preclearing
- Immunoprecipitation
- Washing
- Elution
- Analysis
- Applications
- Pull-down assays
- Analysis
- Cross-linking, label transfer and far–Western blot analysis
- Conclusion
- Chapter 5. Metabolomics and the techniques applicable
- Introduction
- Challenges
- Use of 1D NMR in metabolomic analysis
- Quantitative analysis
- Structural elucidation
- Dynamic studies
- Metabolic profiling
- Biomarker discovery
- Stable isotope tracing
- Quality control in bioprocessing
- Environmental metabolomics
- Pharmacometabolomics
- Food and nutrition studies
- In vivo metabolic imaging
- Use of 2D NMR in metabolomic analysis
- Multivariate analysis
- Data Preprocessing
- Multivariate analysis techniques
- Variable selection
- Validation
- Biomarker identification
- Biological Validation
- Interpretation and reporting
- Identification of metabolites as biomarkers
- Biomarker selection
- Biomarker validation
- Biological Interpretation
- Clinical validation
- Conclusion
- Chapter 6. Advances in metabolomic techniques
- Basics of softwares used in metabolomics
- Statistical analysis
- XCMS and metaXCMS
- metaXCMS: Finding shared alterations among many sample classes
- Data processing workflow using metaXCMS
- MetAlign and LIMSA
- LIMSA
- Discovers and integrates peaks
- Identifies peaks
- Corrects peak areas for overlap
- Quantifies identified species
- Instrument-independent processing
- Text-format MS spectra processing
- Conclusion
- Chapter 7. Ionomics and the techniques applicable
- Introduction
- Techniques for ionomics
- Applications of ionomics
- Limitations and challenges of ionomics
- Conclusion
- Chapter 8. An introduction to systems biology
- Introduction
- Tools, techniques, and approaches used in systems biology
- Applications of systems biology
- Challenges and limitations of systems biology
- Future of systems biology
- Conclusion
- Chapter 9. System biological aspects related to binding and modeling pathways
- Introduction
- Enzyme kinetics
- Michaelis–menten kinetics
- Biological oscillators
- Genetic oscillators
- Cell–cell communication in bacteria
- Quorum sensing
- Steps involved in quorum sensing
- Quorum sensing in gram-positive bacteria
- Quorum sensing in gram-negative bacteria
- Application of quorum sensing
- Limitations of quorum sensing
- Systems approach to model pathways and networks
- Gene regulation at a single-cell level: An intricate dance of molecular control
- Network building analysis for biological processes
- Negative and positive autoregulation
- Chapter 10. Application of omics and systems biology in agriculture and other allied fields
- Metabolomics
- Interactomics
- Types of biomolecular interactions
- Techniques and approaches in interactomics
- Significance and applications
- Challenges and limitations in studying interactomics
- Ionomics
- Analytical techniques required to study ionomics
- Systems biology
- Challenges and limitations of systems biology
- Index
- Edition: 1
- Published: August 13, 2024
- Imprint: Academic Press
- No. of pages: 350
- Language: English
- Paperback ISBN: 9780443219238
- eBook ISBN: 9780443219245
AF
Asmat Farooq
Asmat Farooq is currently pursuing research on “Biochemical characterization and Protein expression analysis” under the supervision of Dr.Sajad Majeed Zargar. Asmat Farooq has qualified National Entrance Test conducted by Indian Council of Agricultural Research, New Delhi for eligibility of lecturer and GATE. Her research interests include insights on crop genomics and phospho-proteomics to understand the biology of stress tolerance in plants. She has published many research articles in many reputed Journals. Her recent article published in Journal of Proteomics provides new insights about phosphorylated proteins as biosensors for stress responses. She has also published some book chapters on crop proteomics. She is an active reviewer for several international journals. She has attended several national and international conferences, workshops, seminars, and training programs.
Affiliations and expertise
Division of Biochemistry, Faculty of Basic Sciences, Sher e Kashmir University Sciences and Technology, Chatha, Jammu, J&K, IndiaSZ
Sajad Majeed Zargar
Sajad Majeed Zargar, Ph.D, is currently an Assistant Professor at Sher-e-Kashmir University of Sciences & Technology in India and visiting Professor at University of Padova, Italy. Dr. Zargar is the recipient of the CREST overseas fellowship from DBT, the Goho grant from Govt. of Japan, and the Erasmus Fellowship from European Union. He is also a member and representative of INPPO (International Plant Proteomics Organisation). His editorial activities and scientific memberships include publishing research and review articles in international journals and is also reviewer.
Affiliations and expertise
Proteomics Laboratory, Division of Biotechnology, Sher-e-Kashmir University of Sciences and Technology, J&K, IndiaPS
Parvaze Ahmad Sofi
Parvaze A. Sofi is a USDA Norman Borlaug Fellow and a Professor at SKUAST-Kashmir. His areas of interest are understanding the role of root architecture and physiological and biochemical responses in drought and heat stress resilience, and he has standardized root architectural studies in crops like rice, wheat, common bean, cowpea, maize and lentil using various laboratory, greenhouse, and field-based screening systems. He has developed two high yielding varieties in common bean and is also associated with the development of high yielding crop varieties of beans, cowpea, chickpea, lentil, moong bean, maize, and wheat.
Affiliations and expertise
Sher-e-Kashmir University of Sciences& Technology, Department of Genetics, IndiaJS
Jebi Sudan
Dr. Jebi Sudan did his M.Sc. in Molecular Biology and Biotechnology (2013) from GB Pant University and his Ph.D. in Biotechnology (2017) from Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu. He has published over fifteen publications in various journals of repute. He was working as an Assistant Professor in JECRC University, Jaipur.
Affiliations and expertise
Division of Biotechnology, Sher-e-Kashmir University of Sciences& Technology, Proteomics Laboratory, IndiaUU
Uneeb Urwat
Dr. Uneeb Urwat did her PhD Biotechnology from Sher-e-Kashmir University of Sciences and Technology. Her core competencies include molecular and cell biology, stress biology and bioinformatics research. She has published a book and 16 papers in reputed journals. She has also guided and taught many undergraduate and postgraduate students.
Affiliations and expertise
Proteomics Laboratory, Division of Biotechnology,Sher-e-Kashmir University of Sciences& Technology, IndiaKH
Khursheed Hussain
Khursheed Hussain, has been serving as Assistant Professor at Sher-e-Kashmir University of Sciences & Technology in India for 13 years. He served as Scientific Officer to Vice Chancellor from 2015-2020. He has published more than 120 research articles, 25 review articles and many books. His contribution in the field of research is in varietal and hybrid development as Principal/Co-breeder of 7 vegetable varieties with other varieties in the pipeline. He has been an advisor of more than 50 PG students and has been invited to give many lectures and trainings.
Affiliations and expertise
Assistant Professor, Division of Vegetable Science. Sher-e-Kashmir University of Sciences& Technology, IndiaRead Concepts and Techniques in OMICS and System Biology on ScienceDirect