Biotechnology Annual Review (eBook)

Front cover 1
Biotechnology Annual Review 4
Copyright page 5
Preface 6
Editorial board 8
List of contributors 10
Contents 14
Chapter 1. The social network of a cell: Recent advances in interactome mapping 16
Introduction 16
Biomolecular interactions in human diseases 17
Charting biomolecular interactions 20
Large-scale approaches: Interactome mapping 21
Measurement of the dynamics of biomolecular interactions: The quantitative methods 29
Conclusions and perspectives 33
Acknowledgments 34
References 34
Chapter 2. Gene expression microarray data analysis demystified 44
Introduction 44
Gene expression microarray platforms 45
Gene expression microarray experiment process 48
Data preprocessing 52
Differential expression analysis 53
Biological interpretation 59
Gene expression microarray data analysis software 60
Cross-platform comparisons 61
Public gene expression data repositories 64
The future 65
Acknowledgements 66
References 66
Chapter 3. UCSC Genome Browser: Deep support for molecular biomedical research 78
Introduction 78
UCSC Genome Browser: The basics - an overview 80
Basic searches in the browser 80
The basic displays: An overview 83
Displaying data types: Visual cues 83
Setting the layout with menu controls 87
Super-tracks for large-scale data 89
Page-wide display controls 89
Display choices are stored 91
Going beyond the image 91
What about the sequencequest 93
Basic sequence searches 95
Advanced exploration with the Table Browser 99
Sample search for all the SNPs in a gene 99
Sample search for filtered SNPs 103
Sample search for SNPs in transcription factor binding sites 103
More details on the Table Browser 106
Custom tracks: Your query as a new track 107
Custom tracks with your own data 108
Community tracks 111
Saving your views as sessions 111
Associated tools at the UCSC site 112
Gene Sorter 112
In-Silico PCR 114
Proteome Browser 116
VisiGene 116
Additional species browsers 116
Coming attractions 118
Next steps 118
Get help from the mailing list and documentation 121
Get training, or train others 121
Acknowledgements 122
References 122
Chapter 4. Potential implications of availability of short amino acid sequences in proteins: An old and new approach to protein decoding and design 124
Introduction 125
Historical and philosophical perspectives on protein sequence information 125
Information extraction from protein sequences using availability scores 132
Current status of availability analysis and future of protein science 147
Conclusion 149
Acknowledgments 150
References 150
Chapter 5. Network models in drug discovery and regenerative medicine 158
Introduction 158
Networks in therapeutic and regenerative medicine 159
Network modelling approaches and tools 166
References 179
Chapter 6. Use of the cauliflower Or gene for improving crop nutritional quality 186
Introduction 186
Carotenoid biosynthesis in plants 188
Regulation of carotenoid biosynthesis in plants 188
Metabolic engineering of carotenoids in crops 192
Functional analysis of the Or gene from cauliflower 193
Creating a metabolic sink is a new strategy to enrich carotenoids in staple food crops 199
Conclusions 200
Acknowledgement 201
References 201
Chapter 7. How to predict and prevent the immunogenicity of therapeutic proteins 206
Introduction 206
Antibody assays 207
Mechanisms of antibody induction 208
Factors influencing the immunogenicity of therapeutic proteins 210
Prediction on the basis of physicochemical characterization 211
Consequences of antibodies to therapeutic proteins 213
Reduction of immunogenicity 214
References 215
Chapter 8. Protein arginine methylation in health and disease 218
Introduction 218
Metabolic pathways 219
Role of protein arginine methyltransferases in growth and differentiation 224
Neurodevelopmental disease 226
Autoimmune disorders 228
Viral disease 229
Cancer 231
Cardiovascular disease 233
Conclusion 233
References 234
Chapter 9. Identification and characterization of a novel cytotoxic protein, parasporin-4, produced by Bacillus thuringiensis A1470 strain 240
Abbreviations 240
General introduction 241
Interaction between a delta-endotoxin of B. thuringiensis and the artificial phospholipid monolayer incorporated with BBM vesicles of Plutella xylostella by SPR-based optical biosensor 244
Formation of the reconstructed monolayer 245
Identification and cloning of two cytotoxic proteins produced by the B. thuringiensis A1470 strain 249
Efficient solubilization, activation, and purification of recombinant parasporin-4 of the B. thuringiensis A1470 strain expressed as inclusion bodies in E. coli 252
Characterization of a novel cytotoxic protein, parasporin-4, produced by the B. thuringiensis A1470 strain 259
Conclusion 263
References 264
Chapter 10. G protein-independent cell-based assays for drug discovery on seven-transmembrane receptors 268
Introduction 268
Receptor desensitization and beta-arrestin recruitment 269
Therapeutic relevance of beta-arrestin-mediated receptor internalization 272
Receptor internalization and beta-arrestin recruitment assays 273
Frizzled receptors and Smoothened 279
Conclusions 282
Acknowledgements 283
References 283
Chapter 11. The application of low shear modeled microgravity to 3-D cell biology and tissue engineering 290
Introduction 290
Technology for 3-D tissue culture 291
Operating principles of the RWV 292
Applications of the RWV 296
Conclusions 305
References 307
Chapter 12. Ethnomedicines and ethnomedicinal phytophores against herpesviruses 312
Introduction 312
The Herpesvirus 313
Control of Herpesvirus infection 314
Conclusions 352
Acknowledgment 353
References 353
Chapter 13. Free radical processes in green tea polyphenols (GTP) investigated by electron paramagnetic resonance (EPR) spectroscopy 364
Abbreviations 364
Introduction to the chemistry of GTP oxidation 365
Biological functions of flavonoids 371
EPR Spectroscopy 375
Investigations of free radical reactions in green tea and GTP 385
Conclusions and forward look 408
Acknowledgments 410
References 410
Chapter 14. Critical review and appraisal of published clinical literature: Useful skill in biotechnology product development 418
Introduction 418
A literature search plan 418
Using a systematic approach to critical appraisal 419
Concluding remarks 425
References 425
Chapter 15. The current status and future potential of personalized diagnostics: Streamlining a customized process 426
Introduction 426
What is personalized medicinequest 427
What are personalized diagnosticsquest 427
What regulations cover personalized diagnosticsquest 429
Current FDA initiatives in personalized regulations 431
Current draft guidances driven by industry 433
Issues in personalized diagnostics 434
Conclusions 436
References 436
Chapter 16. Recent advances in the development of transgenic papaya technology 438
Introduction 438
Transformation systems for papaya 440
Development of economically important traits in papaya by genetic engineering 443
Safety to the environment and food safety 459
Strategies and constraints in the adoption of transgenic papaya technology 464
Concluding remarks 467
Acknowledgements 468
References 468
Index of authors 364
Keyword index 364