Target Discovery and Validation Reviews and Protocols

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Index 353 Recombinant tumor antigens, 301 Recombinase (RAG-1 and RAG-2), 281 Release tags by using tagging enzyme (Bsmfl) of cDNA, 71 Representational difference analysis (RDA), 118, 307 Rescue-suppression-subtractive hybridization, 126 Resistin-like molecule (RELM) alpha and beta, 20 Retroviral vectors, 167 Reverse genetics, 5 Reverse immunology, 322 Reverse phase microarray, 338 Ribozyme display, 342 Ribozyme-expression system, 144 RNA interference (RNAi), 5, 131 mechanism, 132 RNAi technology RNA polymerase III promoter, 177, 8 RNA reference, 59 RT-PCR based expression profiling, 19 S Saccharomyces cerevisiae expression system, 307 Secreted marker, 18 Selection technique, 115 Self-antigens, 293 Self-tolerance, 309 Serial analysis of gene expression (SAGE), 18, 59, 63, 122 bioinformatics analyses of SAGE tags, 77 blunt ending released tags, 71 cleavage of cDNA with anchoring enzyme (NIaIII), 70 electroporation of ligation products and colony PCR, 76 first- and second-strand cDNA synthesis, 70 isolation of ditags, 72 kinasing reaction for linkers, 69 ligate to form ditags, 72 ligating concatemers into pZero, 75 ligating linkers to cDNA, 71 ligation of ditags to form concatemers, 75 Micro SAGE, 60 PCR amplification of Ditags, 72 purification of ditags, 73 release tags by using tagging enzyme (Bsmfl) of cDNA, 71 Serological analysis of recombinant tumor cDNA expression libraries (SEREX), 7, 301, 319, 328 Serological biomarkers, 8 SIM proteins, 22 SIM2-s expression, 23 Single gene disruptions, 34 Single serum biomarkers, 7 Single-minded 2 gene, 21 siRNA libraries, 6 siRNA-liposomes, 311 Site-specific recombinases, 226 Small RNAs, 177 Small-interfering RNA (siRNA), 131, 155, 176 expression libraries, 131 construction of expression vectors, 135 Solid tumors, 16 Somatic cells, 170 Somatic hypermutation, 289 Subclassification, 98 Subnetworks, 50 Subtractive cloning, 116 Subtractive hybridization, 116, 307 Superovulation, 238 Suppression subtractive hybridization (SSH), 118, 307 Suprabasal stratified epithelia, 217 T T7 select TM display, 304 Target discovery, 1, 57, 132 Target validation, 1, 8, 163 Targeted DNA integration, 170 Targeting vectors, design, 220 T-cell, 278 development and maturation, 279, 284 antigen receptor, 281 pre-TCR, 281 TCRαβ, 283 activation, 297 CD8+ cells, 299
354 Index Tetraploid embryos, 239 generation, 239 Thymus-dependent antigens, 290 Thymus-independent antigens, 290 Time-expanded network method, 47, 50 T-lymphocyte-associated antigen (CTLA), 297 TNFα, 270 Tolerizing vaccines, 305 Toll-like receptors, 278 TP53 mutations, 105 Transcriptional gene silencing (TGS), 179 Transcriptional interference, 223 Transdominant negative proteins, 176 Transgene expression vectors, 173 design, 173 Transgenic animal models, 163 Transgenic animals, 9, 163 Transporter associated with antigen presentation (TAP), 295 Transposons, 167 Tryptic digestion, 66 Tumor antigens, 7, 277, 327 discovery, 300 NY-ESO-1, 321 NY-BR-1, 322 NY-BR-62, 321 Tumor biopsies, 93 Tumor escape, 309 Tumor immunology, 300 Tumor infiltrating lymphocyte, 300, 319 Tumor subtypes, robustness, 100 basal-like subtype, 100 Tumor-associated antigens (TAAs), 300 Tumor-specific antigens (TSAs), 300 Two-color fluorescence, 59 Two-dimensional (2D) Western blot, 329 Type 1 immunity, 299 Type 2 immunity, 299 Tyrosinase, 320 U UniGene cluster, 15 W Whole-genome profiling, 94 V Viral vectors, 167 Virtual gene technique, 34, 37 X Xenografting, 10.22 Xenopus, 169 XPD gene, 188 Y Yeast artificial chromosome, 169 Yeast display, 307 Yeast two-hybrid assay, 336
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METHODS IN MOLECULAR BIOLOGY 360 T
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M E T H O D S I N M O L E C U L A R
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© 2007 Humana Press Inc. 999 River
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vi Preface get. Approaches to targe
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viii Contents 10 Transgenic Animal
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x Contributors SAHOHIME MATSUMOTO
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xii Contents of Volume 2 12 Validat
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2 Sioud disease pathogenesis and pe
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4 Sioud A more fruitful approach fo
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6 Sioud both transient and permanen
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8 Sioud serum biomarkers. This syne
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10 Sioud Fig. 2. Schematic of targe
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12 Sioud 13. Magin, T. M. (1998) Le
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Harnessing the Human Genome 15 The
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Harnessing the Human Genome 17 Fig.
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Harnessing the Human Genome 23 The
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Harnessing the Human Genome 27 repr
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Harnessing the Human Genome 29 14.
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Harnessing the Human Genome 31 45.
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34 Imoto et al. (4,5), and Bayesian
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36 Imoto et al. 2. Materials Two ty
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38 Imoto et al. Fig. 3. Graphical v
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40 Imoto et al. Fig. 5. Result of t
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42 Imoto et al. p(D |G) = ∫ p(D,
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44 Imoto et al. β k (k = 1,…,q j
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46 Imoto et al. Fig. 7. Partial res
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48 Imoto et al. Fig. 8. Strategy to
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50 Imoto et al. Fig. 9. (continued)
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52 Imoto et al. Table 3 List of Roo
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54 Imoto et al. 5. De Hoon, M. J. L
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56 Imoto et al. 39. Kamimura, T., S
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58 Beaty et al. cytotoxic drugs and
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60 Beaty et al. Fig. 1. Principles
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62 Beaty et al. oligonucleotide mic
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64 Beaty et al. 3. The 12% polyacry
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66 Beaty et al. 2.3.3. Protein Stai
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68 Beaty et al. 3.1.3. Labeling of
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70 Beaty et al. 1 µL of the anneal
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72 Beaty et al. 4. Phenol:cholorfor
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74 Beaty et al. 19. Wash twice with
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76 Beaty et al. The Following Volum
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78 Beaty et al. using a protein ass
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80 Beaty et al. 6. Shake the gel fo
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82 Beaty et al. Fig. 2. Preparation
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84 Beaty et al. search in. A widely
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86 Beaty et al. 3. Kern, S. E., Hru
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88 Beaty et al. 34. Peters, D. G.,
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5 Molecular Classification of Breas
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Molecular Profiling of Breast Cance
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Fig. 2. (Continued) the right ident
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6 Discovery of Differentially Expre
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Gene Target Discovery 117 In the fi
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Gene Target Discovery 119 sequences
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Gene Target Discovery 121 There is
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Gene Target Discovery 123 digestion
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Gene Target Discovery 125 Fig. 1. P
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Gene Target Discovery 127 5. Sargen
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Gene Target Discovery 129 41. Berry
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132 Matsumoto, Miyagishi, and Taira
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144 Fig. 1. The ribozyme-expression
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146 Sano and Taira 5. 10X L (low-sa
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148 Sano and Taira ribozymes may cl
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150 Fig. 3. A system for the identi
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152 Sano and Taira 4. Notes 1. We r
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9 Production of siRNA- and cDNA-Tra
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Transfected Cell Arrays 157 Fig. 1.
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Transfected Cell Arrays 159 2. The
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Transfected Cell Arrays 161 5. Simp
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164 Houdebine Fig. 1. Different met
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166 Houdebine concentrations become
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168 Houdebine Fig. 2. Major methods
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170 Houdebine integrate into the me
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172 Houdebine 2.2.3. Knock-In Into
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174 Houdebine as insulators. The co
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176 Houdebine Fig. 5. Different met
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178 Houdebine systems. Moreover, st
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180 Houdebine contribute to generat
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182 Houdebine Fig.7. Example of a v
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184 Houdebine more extensively. Tra
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186 Houdebine and stroma. Several o
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188 Houdebine explained at the mole
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190 Houdebine of the intestinal epi
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192 Houdebine interference of the g
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194 Houdebine 17. Whitelaw, C. B. A
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196 Houdebine 51. Bell, A. C., West
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198 Houdebine 86. Carmichael, G. G.
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200 Houdebine 121. Pailhoux, E., Vi
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202 Houdebine 156. Auerbach, A. B.,
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204 Vijayaraj, Söhl, and Magin 1.
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206 Vijayaraj, Söhl, and Magin Fig
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208 Vijayaraj, Söhl, and Magin fil
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210 Table 1 Orthologous Human and M
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212 Table 2 Orthologous Human and M
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242 Table 3 Time Schedule For Aggre
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250 Vijayaraj, Söhl, and Magin 101
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12 The HUVEC/Matrigel Assay An In V
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256 Skovseth, Küchler, and Haralds
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270 Iversen and Sørensen witnessed
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274 Iversen and Sørensen the core
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14 An Overview of the Immune System
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Overview of Immune System 279 diffe
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Overview of Immune System 281 Fig.
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Overview of Immune System 283 then
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Overview of Immune System 285 expre
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Overview of Immune System 287 Once
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Overview of Immune System 289 solub
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Overview of Immune System 291 amino
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Overview of Immune System 293 (unre
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Overview of Immune System 295 Fig.
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Overview of Immune System 297 the c
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Overview of Immune System 299 (44).
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Overview of Immune System 301 demon
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Page 332 and 333: 15 Potential Target Antigens for Im
Page 334 and 335: Tumor Antigen Discovery 321 develop
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Page 340 and 341: 16 Identification of Tumor Antigens
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Page 356 and 357: Protein Arrays 343 The ideal proteo
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Page 360 and 361: Protein Arrays 347 49. Yuko Kawahas
Page 362 and 363: Index 349 Index A Acetyl-CoA carbox
Page 364 and 365: Index 351 conditional by using FRT
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