About Book

Functional genomics is a field of molecular biology that allows the exploration of genes, interactions and protein functions on a universal level. The field of functional genomics attempts to describe the functions and interactions of genes and proteins by making use of genome-wide approaches, in contrast to the gene-by-gene approach of classical molecular biology techniques. It combines data derived from the various processes related to DNA sequence, gene expression, and protein function, such as coding and noncoding transcription, protein translation, protein–DNA, protein–RNA, and protein–protein interactions. Together, these data are used to model interactive and dynamic networks that regulate gene expression, cell differentiation, and cell cycle progression. In functional genomics, the focus is on to use our current knowledge of gene function to develop a model linking genotype to phenotype. This book highlights important matters in the branch of functional genomics, ranging from evaluation of the genetic codes, to understanding of the role of varied genes and proteomic ramifications. This book gives a perspective on primary problems and latest progresses in science and technology in the field of genomics medicine. It explores genomic abnormalities, proteomic pathway, expression alterations, peptidase screening, genomic instability, ant colony algorithm and functional neurogenomics. It deals mainly with their relation to functional genomics and stresses on its particular uses in bio-medicine, agro-food technologies and zoo techniques. It aims to serve as a resource guide for graduates and postgraduates alike and contribute to the growth of the discipline.

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

Chapter 1 Avian Cardiovascular Disease Characteristics, Causes and Genomics.......................................................................................................1

Abstract...................................................................................................1

1. Introduction to the cardiovascular system......................................2

2. Avian cardiovascular genetics............................................................5

3. Conclusions and future directions...................................................17

Acknowledgements.............................................................................19

Conflict of interest..............................................................................19

Chapter 2 Functional Neurogenomics: A New Approach to Study Cognitive Disability in Down Syndrome Brain...................................................29

Abstract.................................................................................................29

1. Introduction..........................................................................................30

2. Generalities of Down syndrome......................................................30

3. Functional neurogenomics: the systemic integration of brain

global gene expression.......................................................................31

4. Cognitive disability and neuroplasticity: our main approach...33

5. Our results............................................................................................41

6. Discussion.............................................................................................45

Chapter 3 Autism Spectrum Disorders: Insights from Genomics...................55

1. Introduction..........................................................................................55

2. Genome wide association and common variants.........................57

3. Rare variants – CNVs and next-generation sequencing..............63

4. Toward a treatment?..........................................................................71

5. Conclusions..........................................................................................72

Chapter 4 Ant Colony Algorithm with Applications in the Field

of Genomics...............................................................................................83

1. Introduction..........................................................................................83

2. General presentation of ant colony algorithm..............................84

3. Conclusions........................................................................................109

Chapter 5 Analysis of Genomic Instability and Tumor-Specific Genetic

Alterations by Arbitrarily Primed PCR.............................................113

1. Introduction........................................................................................113

2. Materials and methods....................................................................115

3. Results and discussion.....................................................................121

4. Conclusions........................................................................................131

5. Acknowledgments.............................................................................131

Chapter 6 Applications of Zymography (Substrate-SDS-PAGE) for Peptidase

Screening in a Post-Genomic Era.......................................................135

1. Introduction........................................................................................135

2. Comments on peptidase screening through substrate-SDSPAGE

..................................................................................................137

3. Practical examples of peptidases sc-reening through SDS-PAGEsubstrate..............................................................................................

143

4. Two-dimensional zymography coupled to peptidase identification

through mass spectrometry: Possibilities and technical

difficulties...........................................................................................153

5. Conclusion..........................................................................................157

Chapter 7 Genomic and Expression Alterations of Tumor Suppressor Genes

in Meningioma Development, Progression and Recurrence ......167

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

2. Molecular alterations involved in the pathogenesis of

meningiomas .....................................................................................170

3. Molecular alterations involved in meningioma progression ..176

4. Altered regions in meningioma progression .............................177

5. Molecular pathology of meningioma recurrence ......................182

6. Signal transduction pathways alter-ed in meningiomas .........185

7. Conclusions .......................................................................................188

8. Acknowledgments ...........................................................................188

Chapter 8 Genomic and Proteomic Pathway Mapping Reveals Signatures of Mesenchymal-Epithelial Plasticity in Inflammatory Breast

Cancer........................................................................................................197

1. Introduction........................................................................................198

2. Defining the signatures of inflammatory breast cancer............204

3. Signature based therapeutic targets in inflammatory breast

cancer .................................................................................................210

4. Summary and conclusions..............................................................212

5. Acknowledgements...........................................................................213

Chapter 9 Genomic Abnormalities in Gliomas..................................................219

1. Introduction ......................................................................................219

2. Tumors of the central nervous system.........................................221

3. Gliomas ..............................................................................................222

4. Single nucleotide polymorphisms and gliomas ........................230

5. Cancer stem cells .............................................................................235

6. Conclusion .........................................................................................237

Citation......................................................................................................251

Index...........................................................................................................253

About Author

Wade Antuña obtained his Ph.D. in Genetics and Genomics from the State University, Chelyabinsk. He is an Assistant Professor at Community College, Kelowna. His work in the field of molecular systematics, conservation genetics, genetics and functional genomics are noted and acclaimed worldwide. Wade is a regular contributor to scientific journals, and has also authored numerous articles and books in the field of molecular biology and genetics. He is a member of several scientific & technical societies. He has attended numerous scientific conferences and symposiums and has presented 8 papers on genomics.