Hyaluronic Acid: Production, Properties, Application in Biology and Medicine

GENOMICS AND PROTEOMICS

Principles, Technologies, and Applications

GENOMICS AND PROTEOMICS

Principles, Technologies, and Applications

Edited by

Devarajan Thangadurai, PhD, and Jeyabalan Sangeetha, PhD

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ABOUT THE EDITORS

Devarajan Thangadurai, PhD

Devarajan Thangadurai, PhD, is Senior Assistant Professor at Karnatak Uni￾versity in South India; President of the Society for Applied Biotechnology; and

General Secretary for the Association for the Advancement of Biodiversity Sci￾ence. In addition, Dr. Thangadurai is Editor-in-Chief of several journals, includ￾ing Biotechnology, Bioinformatics and Bioengineering; Acta Biologica Indica;

Biodiversity Research International; and the Asian Journal of Microbiology.

He received his PhD in Botany from Sri Krishnadevaraya University in South

India. During 2002–2004, he worked as CSIR Senior Research Fellow with

funding from the Ministry of Science and Technology, Government of India.

He served as Postdoctoral Fellow at the University of Madeira, Portugal; Uni￾versity of Delhi, India; and ICAR National Research Centre for Banana, India.

He is the recipient of the Best Young Scientist Award with a Gold Medal from

Acharya Nagarjuna University and the VGST-SMYSR Young Scientist Award

of the Government of Karnataka, Republic of India. He has edited/authored

fifteen books including Genetic Resources and Biotechnology (3 vols.), Genes,

Genomes and Genomics (2 vols.) and Mycorrhizal Biotechnology with publish￾ers of national and international reputation.

Jeyabalan Sangeetha, PhD

Jeyabalan Sangeetha, PhD, is the UGC Kothari Postdoctoral Fellow at Karnatak

University in South India. She earned her a BSc in Microbiology and PhD in

Environmental Sciences from Bharathidasan University, Tiruchirappalli, Tamil

Nadu, India. She holds also an MSc in Environmental Sciences from Bharathiar

University, Coimbatore, Tamil Nadu, India. She is the recipient of the Tamil

Nadu Government Scholarship and the Rajiv Gandhi National Fellowship of

University Grants Commission, Government of India, for her doctoral studies.

She has published approximately 20 manuscripts detailing the effect of pollut￾ants on the environment, and has organized conferences, seminars, workshops,

and lectures. Her main research interests are in the areas of environmental mi￾crobiology and environmental biotechnology, with particular emphasis on solid

waste management, environmental impact assessment, and microbial degrada￾tion of hydrocarbons. Her scientific and community leadership have included

serving as an editor of the journal Biodiversity Research International and Sec￾retary for the Society for Applied Biotechnology.

List of Contributors........................................................................................ix

List of Abbreviations....................................................................................xiii

Preface ........................................................................................................xvii

1. Different Gene Products with a Similar Role in Neuronal Defense

Against Oxidative Stress – Heme Oxygenase System..................................1

Zhi-Gang Jiang and Hossein A. Ghanbari (USA)

2. Embracing Complexity: Searching for Gene-Gene and

Gene Environment Interactions in Genetic Epidemiology .......................19

Alison A. Motsinger and David M. Reif (USA)

3. Elucidation of Proto-Oncogene C-Abl Function with the Use of Mouse

Models and the Disease Model of Chronic Myeloid Leukemia ................59

Jenny F. L. Chau and Baojie Li (Singapore)

4. A Theory on the Molecular Nature of Post-Zygotic Reproductive

Isolation..........................................................................................................95

Francisco Prosdocimi (Brazil)

5. Next Generation Sequencing and Microbiome Evaluation:

Molecular Microbiology and Its Impact on Human Health ...................121

A. Focà, M. C. Liberto, and N. Marascio (Italy)

6. Proteomics and Prostate Cancer................................................................143

Jae-Kyung Myung and Marianne D. Sadar (Canada)

7. RNA Interference Therapeutics – Past, Present and Future ..................175

Jayapal Manikandan, Mahmood Rasool, Muhammad Imran Naseer, Kothandaraman

Narasimhan, Laila Abdullah Damiati, Kalemegam Gauthaman, Sami Bahlas, and

Peter Natesan Pushparaj (Australia, Kingdom of Saudi Arabia)

8. Molecular Mechanisms of Hepatitis C Virus Entry – Impact of

Host Cell Factors for Initiation of Viral Infection ...................................189

Mirjam B. Zeisel and Thomas F. Baumert (France)

9. Molecular Phylogenetics: A Tool for Elucidation of Evolutionary

Processes from Biological Data..................................................................203

Martina Talianova (Czech Republic)

CONTENTS

10. New Insights into the Role of Protein Prenylation and Processing in

Plant Development, Phytohormone Signaling, and Secondary

Metabolism ..................................................................................................251

Dring N. Crowell and Devarajan Thangadurai (India, USA)

11. Mangomics: Information Systems Supporting Advanced Mango

Breeding .......................................................................................................281

David J. Innes, Natalie L. Dillon, Heather E. Smyth, Mirko Karan, Timothy A. Holton,

Ian S. E. Bally, and Ralf G. Dietzgen (Australia)

12. Environmental Genomics: The Impact of Transgenic Crops on

Soil Quality, Microbial Diversity and Plant-Associated Communities..... 309

Jeyabalan Sangeetha, Devarajan Thangadurai, Muniswamy David,

Roopa T. Somanath, Abhishek C. Mundaragi, and Digambarappa P. Biradar (India)

13. Recent Advances in Biotechnology and Genomic Approaches for

Abiotic Stress Tolerance in Crop Plants ...................................................333

Mirza Hasanuzzaman, Rajib Roychowdhury, Joydip Karmakar, Narottam Dey,

Kamrun Nahar, and Masayuki Fujita (Bangladesh, India, Japan)

14. Molecular and Genomic Approaches for Microbial Remediation of

Petroleum Contaminated Soils ..................................................................367

Jeyabalan Sangeetha, Devarajan Thangadurai, Muniswamy David, and

Jadhav Shrinivas (India)

Index.............................................................................................................405

viii Contents

LIST OF CONTRIBUTORS

Sami Bahlas

Rheumatology Department, College of Medicine, King Abdulaziz University, Jeddah - 21589, King￾dom of Saudi Arabia

Ian S. E. Bally

Horticulture and Forestry Sciences, Queensland Department of Agriculture, Fisheries and Forestry,

Mareeba, Australia

Thomas F. Baumert

Université Louis Pasteur, Strasbourg, France

Digambarappa P. Biradar

University of Agricultural Sciences, Dharwad, Karnataka, 580005, India

Jenny F. L. Chau

The Institute of Molecular and Cell Biology, Proteos, 61 Biopolis Drive, Singapore138673, Republic

of Singapore

Dring N. Crowell

Department of Biology, Indiana University - Purdue University Indianapolis, 723 West Michigan

Street, Indianapolis, IN 46202, USA

Laila Abdullah Damiati

King Fahd Medical Research Center, Faculty of Applied Medical Sciences (P.O. Box: 80216), King

Abdulaziz University, Jeddah - 21589, Kingdom of Saudi Arabia

Muniswamy David

Department of Zoology, Karnatak University, Dharwad, Karnataka, 580003, India

Narottam Dey

Department of Biotechnology, Visva-Bharati, Santiniketan-731235, West Bengal, India

Ralf G. Dietzgen

Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia,

Australia

Natalie L. Dillon

Horticulture and Forestry Sciences, Queensland Department of Agriculture, Fisheries and Forestry,

Mareeba, Australia

A. Focà

Microbiology, Department of Health Sciences, School of Medicine, University “Magna Graecia”, Cat￾anzaro, Italy

Masayuki Fujita

Laboratory of Plant Stress Responses, Department of Applied Biological Science, Kagawa University,

2393 Ikenobe, Miki-cho,Kita-gun, Kagawa 761-0795, Japan

Kalemegam Gauthaman

Center of Excellence in Genomic Medicine Research, Faculty of Applied Medical Sciences (P.O. Box:

80216), King Abdulaziz University, Jeddah - 21589, Kingdom of Saudi Arabia

Hossein A. Ghanbari

Panacea Pharmaceuticals, Inc., 207 Perry Parkway, Suite 2, Gaithersburg, MD 20877, USA

Mirza Hasanuzzaman

Department of Agronomy, Faculty of Agriculture, Sher-e-Bangla Agricultural University, Dhaka,

1207, Bangladesh

Timothy A. Holton

Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia,

Australia

David J. Innes

Crop and Food Sciences, Queensland Department of Agriculture, Fisheries and Forestry, St Lucia,

Australia

Zhi-Gang Jiang

Panacea Pharmaceuticals, Inc., 207 Perry Parkway, Suite 2, Gaithersburg, MD 20877, USA

Mirko Karan

Horticulture and Forestry Sciences, Queensland Department of Agriculture, Fisheries and Forestry,

Mareeba, Australia

Joydip Karmakar

Department of Biotechnology, Visva-Bharati, Santiniketan, 731235, West Bengal, India

Baojie Li

The Institute of Molecular and Cell Biology, Proteos, 61 Biopolis Drive, Singapore138673, Republic

of Singapore

M.C. Liberto

Microbiology, Department of Health Sciences, School of Medicine, University “Magna Graecia”, Cat￾anzaro, Italy

Jayapal Manikandan

Faculty of Science, The University of Western Australia (M011), 35 Stirling Highway, Australia

N. Marascio

Microbiology, Department of Health Sciences, School of Medicine, University “Magna Graecia”, Cat￾anzaro, Italy

Alison A. Motsinger

Bioinformatics Research Center, Department of Statistics, North Carolina State University, Raleigh,

NC, USA

Abhishek C. Mundaragi

Department of Botany, Karnatak University, Dharwad, Karnataka, 580003, India

Jae-Kyung Myung

British Columbia Cancer Agency, Genome Sciences Centre, 675 West 10th Avenue, Vancouver, British

Columbia, V5Z 1L3, Canada

Kamrun Nahar

Laboratory of Plant Stress Responses, Department of Applied Biological Science, Kagawa University,

2393 Ikenobe, Miki-cho,Kita-gun, Kagawa 761-0795, Japan

x List of Contributors

Kothandaraman Narasimhan

Center of Excellence in Genomic Medicine Research, Faculty of Applied Medical Sciences (P.O. Box:

80216), King Abdulaziz University, Jeddah - 21589, Kingdom of Saudi Arabia

Muhammad Imran Naseer

Center of Excellence in Genomic Medicine Research, Faculty of Applied Medical Sciences (P.O. Box:

80216), King Abdulaziz University, Jeddah - 21589, Kingdom of Saudi Arabia

Francisco Prosdocimi

Laboratório de Biodados, Depto. Bioquímica e Imunologia, ICB-UFMG, Av. Antônio Carlos 6627 CP

486, 31.270-010 BH-MG, Brazil

Peter Natesan Pushparaj

Center of Excellence in Genomic Medicine Research, Faculty of Applied Medical Sciences (P.O. Box:

80216), King Abdulaziz University, Jeddah - 21589, Kingdom of Saudi Arabia

Mahmood Rasool

Center of Excellence in Genomic Medicine Research, Faculty of Applied Medical Sciences (P.O. Box:

80216), King Abdulaziz University, Jeddah - 21589, Kingdom of Saudi Arabia

David M. Reif

National Center for Computational Toxicology, U.S. Environmental Protection Agency, Research Tri￾angle Park, NC, USA

Rajib Roychowdhury

Department of Biotechnology, Visva-Bharati, Santiniketan, 731235, West Bengal, India

Marianne D. Sadar

British Columbia Cancer Agency, Genome Sciences Centre, 675 West 10th Avenue, Vancouver, British

Columbia, V5Z 1L3, Canada

Jeyabalan Sangeetha

Department of Zoology, Karnatak University, Dharwad, Karnataka, 580003, India

Jadhav Shrinivas

Department of Zoology, Karnatak University, Dharwad, Karnataka, 580003, India

Heather E. Smyth

Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia,

Australia

Roopa T. Somanath

Department of Botany, Karnatak University, Dharwad, Karnataka, 580003, India

Martina Talianova

Laboratory of Plant Developmental Genetics, Institute of Biophysics, Czech Academy of Sciences,

Kralovopolska 135, 61265 Brno, Czech Republic

Devarajan Thangadurai

Department of Botany, Karnatak University, Dharwad, Karnataka, 580003, India

Mirjam B. Zeisel

Inserm, U748, Strasbourg, France

List of Contributors xi

LIST OF ABBREVIATIONS

AIC Akaike’s Information Criterion

ALF Acute Liver Failure

ALS Amyotrophic Lateral Sclerosis

ANOVA Analysis of Variance

ARE Antioxidant Response Element

BCR Breakpoint Cluster Region

BIC Bayesian Information Criterion

CART Classification and Regression Trees

CID Collision-Induced Dissociation

CML Chronic Myelogenous Leukemia

CNS Central Nerve System

CPM Combinatorial Partitioning Method

CRFs Circulating Recombinant Forms

CSS Chi-Square Subset

DBD DNA-Binding Domain

DICE Detection of Informative Combined Effect

DM Dobzhansky-Muller

EBV Epstein-Barr Virus

EGF Epidermal Growth Factor

ERK Extracellular Signal-Regulated Kinase

FBAT Family Based Association Test

FDA Food and Drug Administration

FDR False Discovery Rate

FGS First-Generation Sequencing

FITF Focused Interaction Testing Framework

FRET Fluorescence Resonance Energy Transfer

GA Genetic Algorithms

GLMs Generalized Linear Models

GPNN Genetic Programming Neural Networks

GST Glutathione S-Transferase

GTR Time Reversible Models

HIV Human Immunodeficiency Virus

HMP Human Microbiome Project

HO Heme Oxygenase

HTS High-Throughput Sequencing