Target Discovery and Validation Reviews and Protocols

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Keratin Transgenics and Knockouts 245 role in skin integrity and in epidermolysis bullosa simplex. Mol. Biol. Cell 12, 1775–1789. 22. Coulombe, P. A. and Omary, M. B. (2002) ‘Hard’ and ‘soft’ principles defining the structure, function and regulation of keratin intermediate filaments. Curr. Opin. Cell Biol. 14, 110–122. 23. Ku, N. O. and Omary, M. B. (2000) Keratins turn over by ubiquitination in a phosphorylation-modulated fashion. J. Cell Biol. 149, 547–552. 24. Steinert, P. M. and Marekov, L. N. (1995) The proteins elafin, filaggrin, keratin intermediate filaments, loricrin, and small proline-rich proteins 1 and 2 are isodipeptide cross-linked components of the human epidermal cornified cell envelope. J. Biol. Chem. 270, 17,702–17,711. 25. Abe, M. and Oshima, R. G. (1990) A single human keratin 18 gene is expressed in diverse epithelial cells of transgenic mice. J. Cell Biol. 111, 1197–1206. 26. Neznanov, N., Umezawa, A., and Oshima, R. G. (1997) A regulatory element within a coding exon modulates keratin 18 gene expression in transgenic mice. J. Biol. Chem. 272, 27,549–27,557. 27. Rhodes, K. and Oshima, R. G. (1998) A regulatory element of the human keratin 18 gene with AP-1-dependent promoter activity. J. Biol. Chem. 273, 26,534–26,542. 28. Willoughby, D. A., Vilalta, A., and Oshima, R. G. (2000) An Alu element from the K18 gene confers position-independent expression in transgenic mice. J. Biol. Chem. 275, 759–768. 29. Wen, F., Cecena, G., Munoz-Ritchie, V., Fuchs, E., Chambon, P., and Oshima, R. G. (2003) Expression of conditional cre recombinase in epithelial tissues of transgenic mice. Genesis 35, 100–106. 30. Sinha, S., Degenstein, L., Copenhaver, C., and Fuchs, E. (2000) Defining the regulatory factors required for epidermal gene expression. Mol. Cell Biol. 20, 2543–2555. 31. Sugihara, T. M., Kudryavtseva, E. I., Kumar, V., Horridge, J. J., and Andersen, B. (2001) The POU domain factor Skin-1a represses the keratin 14 promoter independent of DNA binding. A possible role for interactions between Skn-1a and CREB-binding protein/p300. J. Biol. Chem. 276, 33,036–33,044. 32. Lu, H., Hesse, M., Peters, B., and Magin, T. M. (2005) Type II keratins precede type I keratins during early embryonic development. Eur. J. Cell Biol. 84, 709–718. 33. Ameen, N. A., Figueroa, Y., and Salas, P. J. (2001) Anomalous apical plasma membrane phenotype in CK8-deficient mice indicates a novel role for intermediate filaments in the polarization of simple epithelia. J. Cell Sci. 114, 563–575. 34. Magin, T. M. (1998) Lessons from keratin transgenic and knockout mice. Subcell. Biochem. 31, 141–172. 35. Lloyd, C., Yu, Q. C., Cheng, J., et al. (1995) The basal keratin network of stratified squamous epithelia: defining K15 function in the absence of K14. J. Cell Biol. 129, 1329–1344. 36. Tong, X. and Coulombe, P. A. (2004) A novel mouse type I intermediate filament gene, keratin 17n (K17n), exhibits preferred expression in nail tissue. J. Invest. Dermatol. 122, 965–970.
246 Vijayaraj, Söhl, and Magin 37. Herzog, F., Winter, H., and Schweizer, J. (1994) The large type II 70-kDa keratin of mouse epidermis is the ortholog of human keratin K2e. J. Invest. Dermatol. 102, 165–170. 38. Swensson, O., Langbein, L., McMillan, J. R., et al. (1998) Specialized keratin expression pattern in human ridged skin as an adaptation to high physical stress. Br. J. Dermatol. 139, 767–775. 39. Freedberg, I. M., Tomic-Canic, M., Komine, M., and Blumenberg, M. (2001) Keratins and the keratinocyte activation cycle. J. Invest. Dermatol. 116, 633–640. 40. McGowan, K. and Coulombe, P. A. (1998a) The wound repair-associated keratins 6, 16, and 17. Insights into the role of intermediate filaments in specifying keratinocyte cytoarchitecture. Subcell. Biochem. 31, 173–204. 41. McGowan, K. M. and Coulombe, P. A. (1998b) Onset of keratin 17 expression coincides with the definition of major epithelial lineages during skin development. J. Cell Biol. 143, 469–486. 42. Kasper, M. (1992) Patterns of cytokeratins and vimentin in guinea pig and mouse eye tissue: evidence for regional variations in intermediate filament expression in limbal epithelium. Acta Histochem. 93, 319–332. 43. Brock, J., McCluskey, J., Baribault, H., and Martin, P. (1996) Perfect wound healing in the keratin 8 deficient mouse embryo. Cell Motil. Cytoskeleton 35, 358–366. 44. Jackson, B. W., Grund, C., Schmid, E., Burki, K., Franke, W. W., and Illmensee, K. (1980) Formation of cytoskeletal elements during mouse embryogenesis. Intermediate filaments of the cytokeratin type and desmosomes in preimplantation embryos. Differentiation 17, 161–179. 45. Mazzalupo, S., Wong, P., Martin, P., and Coulombe, P. A. (2003) Role for keratins 6 and 17 during wound closure in embryonic mouse skin. Dev. Dyn. 226, 356–365. 46. Mills, A. A., Zheng, B., Wang, X. J., Vogel, H., Roop, D. R., and Bradley, A. (1999) p63 is a p53 homologue required for limb and epidermal morphogenesis. Nature 398, 708–713. 47. Lane, E. B. and McLean, W. H. (2004) Keratins and skin disorders. J. Pathol. 204, 355–366. 48. Porter, R. M. and Lane, E. B. (2003) Phenotypes, genotypes and their contribution to understanding keratin function. Trends Genet. 19, 278–285. 49. Yoneda, K., Furukawa, T., Zheng, Y. J., et al. (2004) An autocrine/paracrine loop linking keratin 14 aggregates to tumor necrosis factor alpha-mediated cytotoxicity in a keratinocyte model of epidermolysis bullosa simplex. J. Biol. Chem. 279, 7296–7303. 50. D’Alessandro, M., Russell, D., Morley, S. M., Davies, A. M., and Lane, E. B. (2002) Keratin mutations of epidermolysis bullosa simplex alter the kinetics of stress response to osmotic shock. J. Cell Sci. 115, 4341–4351. 51. Owens, D. W. and Lane, E. B. (2004) Keratin mutations and intestinal pathology. J. Pathol. 204, 377–385.
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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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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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Overview of Immune System 307 some
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Overview of Immune System 309 sera
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Overview of Immune System 313 measu
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Overview of Immune System 315 42. H
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Overview of Immune System 317 74. D
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15 Potential Target Antigens for Im
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Tumor Antigen Discovery 321 develop
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Tumor Antigen Discovery 323 panel b
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Tumor Antigen Discovery 325 16. Joc
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16 Identification of Tumor Antigens
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Immunoproteomics 329 by “shot gun
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Immunoproteomics 331 isoelectric fo
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Immunoproteomics 333 3. 2D-PAGE is
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17 Protein Arrays A Versatile Toolb
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Protein Arrays 337 Table 1 Classifi
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Protein Arrays 339 fractions from c
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Protein Arrays 341 combinatorial sc
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Protein Arrays 343 The ideal proteo
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Protein Arrays 345 18. Cekaite, H.
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Protein Arrays 347 49. Yuko Kawahas
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Index 349 Index A Acetyl-CoA carbox
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Index 351 conditional by using FRT
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Index 353 Recombinant tumor antigen
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