About Book

Genetics and genetic engineering provide powerful tools for the study of gene function in both cells and organisms. Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product. These products are often proteins, but in non-protein coding genes such as ribosomal RNA genes or transfer RNA genes, the product is a functional RNA. Molecular biology is a branch of science concerning biological activity at the molecular level. As a part of biochemistry, gene biotechnology amalgamates the elements of genetics and biotechnology to understand and experiment with genes in order to develop better genetically modified and cloned organisms. Gene isolation and gene cloning is also a part of gene biotechnology. This book is designed to provide in-depth information about the various concepts, theories, techniques and methods related to gene biotechnology. It deals with gene expression, toxicity, molecular cloning, immunological characterization, phylogenetic analysis, microarray experiment, genomic copy and chronic fatigue syndrome. It presents chapters which deal with the most important topics in this field and emerging at a rapid pace; the contents of this book will help the readers understand the modern concepts of the subject. Those in search of information to further their knowledge will be greatly assisted by this book.

Preface............................................................................................................v

Chapter 1 Gene Expression in Chronic Fatigue Syndrome.................................1

1. Introduction ..........................................................................................1

2. Molecular studies .................................................................................2

3. Conclusion ...........................................................................................22

Chapter 2 Molecular Portrait of Clear Cell Renal Cell Carcinoma: An Integrative Analysis of Gene Expression and Genomic Copy Number Profiling......................................................................................48

1. Introduction ........................................................................................48

2. Methods ...............................................................................................53

3. Result ...................................................................................................57

4. Discussion ...........................................................................................69

5. Conclusion ...........................................................................................76

6. Acknowledgment ...............................................................................77

Chapter 3 Quantification of Gene Expression Based on Microarray Experiment..................................................................................................91

1. Introduction ........................................................................................91

2. Methods to quantifying mRNA level ............................................94

3. Microarray technology ......................................................................97

4. The DNA microarray experiment ..................................................99

5. Image processing .............................................................................104

6. Preprocessing of cDNA microarray data .......................................110

7. Differentially gene expression .......................................................115

8. R and bioconductor packages .......................................................117

9. Conclusion .........................................................................................124

Chapter 4 Molecular Cloning, Expression Pattern, and Phylogenetic Analysis

of the Lysyl-tRNA Synthetase Gene from the Chinese Oak

Silkworm Antheraea pernyi..................................................................131

1. Introduction ......................................................................................131

2. Materials and methods ...................................................................132

3. Results and discussion ...................................................................134

4. Conclusion .........................................................................................140

5. Acknowledgment .............................................................................140

Chapter 5 Molecular Cloning, Expression, Purification and Immunological

Characterization of Proteins Encoded by Regions of Difference

Genes of Mycobacterium tuberculosis...............................................144

1. Introduction ......................................................................................144

2. Identification of M. tuberculosis-specific genomic regions and

encoded antigens .............................................................................146

3. Molecular cloning, expression, purification and immunological

characterization of proteins encoded by RD genes ..................148

4. Potential of the purified recombinant RD proteins as

M. tuberculosis-specific skin test antigens ...................................153

5. Cloning, expression and immunogenicity of RD genes in DNA

vaccine vectors ..................................................................................154

6. Conclusions .......................................................................................159

7. Acknowledgements .........................................................................160

Chapter 6 Molecular Cloning, Characterization, Expression Analysis and

Chromosomal Localization of the Gene Coding for the Porcine

αIIb Subunit of the αIIbβ3 Integrin Platelet Receptor.................167

1. Introduction ......................................................................................167

2. Material and methods .....................................................................169

3. Results ................................................................................................175

4. Discussion .........................................................................................193

5. Conclusion .........................................................................................198

Chapter 7 Gene Expressions of the Dhb, Vtg, Arnt, CYP4, CYP314 in Daphnia

magna Induced by Toxicity of Glyphosate and Methidathion

Pesticides...................................................................................................206

1. Introduction ......................................................................................206

2. Experimental methods ....................................................................208

3. Results and discussion ...................................................................211

4. Conclusions .......................................................................................223

5. Acknowledgements .........................................................................223

Chapter 8 Gene Expression Analysis Using RNA-Seq from Organisms

Lacking Substantial Genomic Resources..........................................227

1. Introduction........................................................................................227

2. De Novo sequence assembly and expression analysis with NGS

data......................................................................................................228

3. Conclusion..........................................................................................253

Citation......................................................................................................259

Index...........................................................................................................261

About Author

Sharlton Carlyle pursued her Ph.D. in Genetics from Public Science University, La Harpe. Her primary areas of scholarly and research interests lie in the fields of gene expression and protein binding. She is serving as a Research Associate at Technical Institute, Naples. She has contributed numerous articles and book chapters in the field of genetics. She is also an active member and a regular contributor to several scientific clubs and societies. Carlyle has travelled and lectured extensively throughout Europe and United States; primarily for higher education programmes.