This item is in: Biomedicine > Genetics and genomics

Concepts and techniques in genomics and proteomics

N Saraswathy and P Ramalingam, Kumaraguru College of Technology, India

Woodhead Publishing Series in Biomedicine No. 5

 - provides definitions for key concepts
 - case studies are included to illustrate ideas
 - important points to remember are noted
 - contains suggestions for recent references and web site addresses

Concepts and techniques in genomics and proteomics covers the important concepts of high-throughput modern techniques used in the genomics and proteomics field. Each technique is explained with its underlying concepts, and simple line diagrams and flow charts are included to aid understanding and memory. A summary of key points precedes each chapter within the book, followed by detailed description in the subsections. Each subsection concludes with suggested relevant original references.

ISBN 1 907568 10 7
ISBN-13: 978 1 907568 10 7
July 2011
268 pages  234 x 156mm  hardback  
£70.00 / US$120.00 / €85.00

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About the authors

Dr Nachimuthu Saraswathy is currently Associate Professor at the Department of Biotechnology, Kumaraguru College of Technology. She teaches courses on Molecular Biology, Genetic Engineering, and Plant Biotechnology, as well as Genomics and Proteomics. Dr Saraswathy gained her Ph.D. in Molecular Biology from the National Centre for Plant Biotechnology, New Delhi. She has published several articles in journals of biotechnology and biochemistry.

Mr Ponnusamy Ramalingam is Associate Professor at the Department of Biotechnology, Kumaraguru College of Technology. He received his M.Sc. In Biochemistry from Gulbarga University and Mtech in Biotechnology from Anna University. He has also taught and researched in institutions such as Kongu Engineering College and PNC&KR College, and has contributed several published journal articles.

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Contents

Introduction to genes and genomes
 - Introduction
 - The cell
 - Mendel’s contributions
 - The chromosomal theory of inheritance
 - The chemical nature of genetic material
 - Composition and structure of DNA
 - The central dogma of life
 - Genomes of prokaryotes and eukaryotes
 - The molecular structure of the gene
 - Conclusion
 - Review questions and answers
 - Recommended reading

The human genome project
 - The history of the HGP
 - The budget for the HGP
 - Goals of the HGP
 - Laboratories and investigators involved in the HGP
 - The Human Genome Organization (HUGO)
 - Salient findings of the HGP
 - Potential applications of the HGP
 - Post-HGP challenges
 - Ethical, legal, social issues (ELSI) related to the HGP
 - The international HapMap Project
 - Review questions and answers
 - Recommended reading

Genomes of model organisms
 - Introduction
 - The viral genome
 - Bacterial genomes
 - Fungal genomes
 - Worm genome: Caenorhabditis elegans
 - Fruit fly: Drosophila melanogaster
 - Plant genome
 - Animal genome
 - The Microbial Genome Project
 - Review questions and answers
 - Recommended reading

High capacity vectors
 - Introduction
 - Cosmid vectors
 - Fosmid vectors
 - Bacteriophage P1 derived vector
 - P1 derived artificial chromosome (PAC)
 - Bacterial artificial chromosomes (BAC)
 - Yeast artificial chromosome (YAC)
 - Review questions and answers
 - Recommended reading

DNA sequencing methods
 - The history of DNA sequencing
 - Steps in DNA sequencing
 - Chemical degradation method of DNA sequencing
 - The chain termination method of DNA sequencing
 - Advances in DNA sequencing methods
 - New sequencing methods
 - Next generation sequencing methods
 - Review questions and answers
 - Recommended reading

Genome mapping
 - Introduction
 - Importance of genome mapping in the context of genome sequencing
 - Genetic mapping
 - Genetic mapping in humans
 - Physical mapping methods
 - Review questions and answers
 - Recommended reading

Genome sequencing methods
 - Introduction
 - The clone-by-clone genome sequencing method
 - The whole genome shotgun sequencing method
 - Error control in genome sequencing
 - Review questions and answers
 - Recommended reading

Genome sequence assembly and annotation
 - Introduction
 - Clone contig assembly
 - Genome assembly program
 - Gaps and gap closing methods
 - Draft and finished genome sequences
 - Genome annotation
 - Comparative genomics
 - Review questions and answers
 - Recommended reading

Functional genomics
 - Introduction
 - Northern blotting
 - Subtractive hybridization
 - Differential Display Reverse Transcription
 - PCR (DDRT-PCR)
 - Representational Difference Analysis (RDA)
 - Serial Analysis Gene Expression (SAGE)
 - Microarray technology
 - Review questions and answers
 - Recommended reading

Introduction to proteomics
 - Introduction
 - Traditional route of protein study
 - Protein isolation methods
 - Branches of proteomics
 - Characteristics of proteomics
 - Review questions and answers
 - Recommended reading

Two-dimensional gel electrophoresis of proteins
 - Introduction
 - Principles of 2D-PAGE
 - 2D-PAGE apparatus
 - Sample preparation
 - First-dimensional separation by isoelectric focusing
 - Equilibration
 - Second-dimensional separation by SDS-PAGE
 - Detection of proteins on 2D-PAGE gels
 - Image analysis
 - Application of 2D-PAGE in proteomics
 - Review questions and answers
 - Recommended reading

Mass spectrometry for proteomics
 - Introduction
 - History of the mass spectrometer
 - Mass spectrometer
 - Protein sample preparation for MS analysis
 - Applications of MS proteomics
 - Review questions and answers
 - Recommended reading

Protein Identifi cation by Peptide Mass Fingerprinting (PMF)
 - Introduction
 - Principles of peptide mass fingerprinting
 - Protein preparation for PMF
 - Mass spectrometric analysis of peptide fragments
 - Data analysis and identification of protein
 - Review question and answer
 - Recommended reading

Protein sequencing techniques
 - Introduction
 - Preparation of protein sample for sequencing
 - Steps in protein sequencing
 - Protein sequencing by Edman degradation
 - De novo protein sequencing by mass spectrometry
 - Review questions and answers
 - Recommended reading

Phosphoproteomics
 - Post-translational modifications of proteins
 - Phosphoproteomics
 - Phosphoproteins enrichment methods
 - Mass spectrometry for phosphoprotein identification
 - Review questions and answers
 - Recommended reading

Glycoproteomics
 - Glycoproteins
 - Glycoprotein enrichment methods
 - Mass spectrometric analysis of glycoproteins
 - Importance of glycoproteins in human diseases
 - Review questions and answers
 - Recommended reading

Conclusion

Glossary