Principles of genomics and proteomics / Rakeeb Ahmad Mir, Sheikh Mansoor Shafi, Sajad Majeed Zargar. -- Cambridge MA : Elsevier, 2023. – (58.21/M671)

Contents

About the authors
Foreword  xvii
Preface  xix
Acknowledgments  xxi
CHAPTER 1  Understanding the OMICS techniques: an introduction to genomics and proteomics  1
1 Introduction to genomics  1
2 Genomes of the eukaryotes--nuclear and organelle genomes  7
3 Organization of eukaryotic genome  10
4 Organelle genome editing  18
5 Introduction to proteomics  20
6 Proteome profiling  25
7 Conclusion  26
References  26
CHAPTER 2 Genome mapping  29
1 Introduction  29
2 Markers  30
3 Physical mapping  40
References  44
CHAPTER 3 Analysis of genomes--I
1 Introduction  47
2 Sangers sequencing/chain-termination sequencing method  48
3 Whole-genome shotgun sequencing  50
4 Hierarchical shotgun sequencing  50
5 Next-generation sequencing methods  51
6 Genome sequencing projects  55
7 Conclusion  62
References  63
CHAPTER 4 Analysis of genomes--II
1 Introduction  65
2 DNA footprinting/deoxyribonuclease I (DNase I) protection mapping
3 Gel retardation assay or electrophoretic mobility shift assay or band shift assay
4 Chromatin immunoprecipitation and its variants  73
5 Conclusion  83
References  83
CHAPTER 5  Nutrigenomics: Insights into the influence of nutrients on functional dynamics of genomes  89
1 Introduction  89
2 Nutrigenomics studies of selected crop plants--a repository of functional foods
3 Conclusion  104
References  105
CHAPTER 6 Analysis of proteomes--I
1 Polyacrylamide gel electrophoresis and SDS-PAGE  111
2 Isoelectric focusing gels  117
3 2D gel electrophoresis-combining SDS-PAGE and IEF for unison gel-based identification of proteins on the basis of size and charge  118
4 MALDI-TOF mass spectrometry  120
5 Isotope-coded affinity tags  125
6 Isotope-coded protein labeling  127
7 Isobaric tags for relative and absolute quantification  128
8 The tandem mass tag  131
9 Stable isotopic labeling of amino acids in cell culture  131
10 Discussion  135
References  135
CHAPTER 7 Analysis of proteomes--II
1 Introduction  139
2 Ultraviolet and visible light spectroscopy  139
3 Fluorescence spectroscopy  146
4 Nuclear magnetic resonance spectroscopy  149
5 X-ray diffraction  154
6 Circular dichroism  159
7 Conclusion  161
References  161
CHAPTER 8 Analysis of proteomes--III
1 Protein structure prediction  165
2 Protein secondary and tertiary structure predictions  165
3 Homology or template-based modeling  166
4 Protein threading  169
5 Ab initio protein structure predictions  170
6 Conclusions  173
References  173
CHAPTER 9 Analysis of proteomes--IV
1 Introduction  177
2 Yeast 2-hybrid system  177
3 Principle  179
4 Advantages and limitations  180
5 Limitations of Y2H assays  180
6 Phage display  180
7 Application  181
8 Protein chips  182
9 Applications of protein microarrays  184
10 Conclusion and future prospective  187
References  188
CHAPTER 10 Beyond genomics and proteomics  191
1 Introduction
2 Transcriptomics
3 Metabolomics
4 Interactomics  204
5 Lipidomics  209
6 Metagenomics  213
7 Ionomics  218
8 Connectomics  221
9 Conclusion  225
References  226
Further reading  242
Index  245