Target Discovery and Validation Reviews and Protocols

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Keratin Transgenics and Knockouts 247 52. Zatloukal, K., Stumptner, C., Fuchsbichler, A., et al. (2004) The keratin cytoskeleton in liver diseases. J. Pathol. 204, 367–376. 53. Baribault, H., Penner, J., Iozzo, R. V., and Wilson-Heiner, M. (1994) Colorectal hyperplasia and inflammation in keratin 8-deficient FVB/N mice. Genes Dev. 8, 2964–2973. 54. Baribault, H., Price, J., Miyai, K., and Oshima, R. G. (1993) Mid-gestational lethality in mice lacking keratin 8. Genes Dev. 7, 1191–1202. 55. Jaquemar, D., Kupriyanov, S., Wankell, M., et al. (2003) Keratin 8 protection of placental barrier function. J. Cell Biol. 161, 749–756. 56. Toivola, D. M., Krishnan, S., Binder, H. J., Singh, S. K., and Omary, M. B. (2004) Keratins modulate colonocyte electrolyte transport via protein mistargeting. J. Cell Biol. 164, 911–921. 57. Habtezion, A., Toivola, D. M., Butcher, E. C., and Omary, M. B. (2005) Keratin- 8-deficient mice develop chronic spontaneous Th2 colitis amenable to antibiotic treatment. J. Cell Sci. 118, 1971–1980. 58. Satoh, M. I., Hovington, H., and Cadrin, M. (1999) Reduction of cytochemical ecto-ATPase activities in keratin 8-deficient FVB/N mouse livers. Med. Electron Microsc. 32, 209–212. 59. Caulin, C., Ware, C. F., Magin, T. M., and Oshima, R. G. (2000) Keratin-dependent, epithelial resistance to tumor necrosis factor-induced apoptosis. J. Cell Biol. 149, 17–22. 60. Gilbert, S., Loranger, A., Daigle, N., and Marceau, N. (2001) Simple epithelium keratins 8 and 18 provide resistance to Fas-mediated apoptosis. The protection occurs through a receptor-targeting modulation. J. Cell Biol. 154, 763–773. 61. Inada, H., Izawa, I., Nishizawa, M., et al. (2001) Keratin attenuates tumor necrosis factor-induced cytotoxicity through association with TRADD. J. Cell Biol. 155, 415–426. 62. Toivola, D. M., Nieminen, M. I., Hesse, M., et al. (2001) Disturbances in hepatic cell-cycle regulation in mice with assembly-deficient keratins 8/18. Hepatology 34, 1174–1183. 63. Tamai, Y., Ishikawa, T., Bosl, M. R., et al. (2000) Cytokeratins 8 and 19 in the mouse placental development. J. Cell Biol. 151, 563–572. 64. Hesse, M., Franz, T., Tamai, Y., Taketo, M. M., and Magin, T. M. (2000) Targeted deletion of keratins 18 and 19 leads to trophoblast fragility and early embryonic lethality. EMBO J. 19, 5060–5070. 65. Hesse, M., Watson, E. D., Schwaluk, T., and Magin, T. M. (2005) Rescue of keratin 18/19 doubly deficient mice using aggregation with tetraploid embryos. Eur. J. Cell Biol. 84, 355–361. 66. Andra, K., Lassmann, H., Bittner, R., et al. (1997) Targeted inactivation of plectin reveals essential function in maintaining the integrity of skin, muscle, and heart cytoarchitecture. Genes Dev. 11, 3143–3156. 67. Guo, L., Degenstein, L., Dowling, J., et al. (1995) Gene targeting of BPAG1: abnormalities in mechanical strength and cell migration in stratified epithelia and neurologic degeneration. Cell 81, 233–243.
248 Vijayaraj, Söhl, and Magin 68. Kowalczyk, A. P., Bornslaeger, E. A., Norvell, S. M., Palka, H. L., and Green, K. J. (1999) Desmosomes: intercellular adhesive junctions specialized for attachment of intermediate filaments. Int. Rev. Cytol. 185, 237–302. 69. Smith, E. A. and Fuchs, E. (1998) Defining the interactions between intermediate filaments and desmosomes. J. Cell Biol. 141, 1229–1241. 70. Hutton, E., Paladini, R. D., Yu, Q. C., Yen, M., Coulombe, P. A., and Fuchs, E. (1998) Functional differences between keratins of stratified and simple epithelia. J. Cell Biol. 143, 487–499. 71. Fuchs, E. (1995) Keratins and the skin. Annu. Rev. Cell Dev. Biol. 11, 123–153. 72. Cao, T., Longley, M. A., Wang, X. J., and Roop, D. R. (2001) An inducible mouse model for epidermolysis bullosa simplex: implications for gene therapy. J. Cell Biol. 152, 651–656. 73. Berton, T. R., Wang, X. J., Zhou, Z., et al. (2000) Characterization of an inducible, epidermal-specific knockout system: differential expression of lacZ in different Cre reporter mouse strains. Genesis 26, 160–161. 74. Fuchs, E. and Green, H. (1980) Changes in keratin gene expression during terminal differentiation of the keratinocyte. Cell 19, 1033–1042. 75. Reichelt, J., Bussow, H., Grund, C., and Magin, T. M. (2001) Formation of a normal epidermis supported by increased stability of keratins 5 and 14 in keratin 10 null mice. Mol. Biol. Cell 12, 1557–1568. 76. van Hemert, M. J., Steensma, H. Y., and van Heusden, G. P. (2001) 14-3-3 proteins: key regulators of cell division, signalling and apoptosis. Bioessays 23, 936–946. 77. Reichelt, J. and Magin, T. M. (2002) Hyperproliferation, induction of c-Myc and 14-3-3sigma, but no cell fragility in keratin-10-null mice. J. Cell Sci. 115, 2639–2650. 78. Paramio, J. M. and Jorcano, J. L. (2002) Beyond structure: do intermediate filaments modulate cell signalling? Bioessays 24, 836–844. 79. Reichelt, J., Breiden, B., Sandhoff, K., and Magin, T. M. (2004a) Loss of keratin 10 is accompanied by increased sebocyte proliferation and differentiation. Eur. J. Cell Biol. 83, 747–759. 80. Reichelt, J., Furstenberger, G., and Magin, T. M. (2004b) Loss of keratin 10 leads to mitogen-activated protein kinase (MAPK) activation, increased keratinocyte turnover, and decreased tumor formation in mice. J. Invest. Dermatol. 123, 973–981. 81. Porter, R. M., Leitgeb, S., Melton, D. W., Swensson, O., Eady, R. A., and Magin, T. M. (1996) Gene targeting at the mouse cytokeratin 10 locus: severe skin fragility and changes of cytokeratin expression in the epidermis. J. Cell Biol. 132, 925–936. 82. Reichelt, J., Bauer, C., Porter, R., Lane, E., and Magin, V. (1997) Out of balance: consequences of a partial keratin 10 knockout. J. Cell Sci. 110 (18), 2175–2186. 83. Elias, P., Man, M. Q., Williams, M. L., Feingold, K. R., and Magin, T. (2000) Barrier function in K-10 heterozygote knockout mice. J. Invest. Dermatol. 114, 396, 397. 84. Reichelt, J., Doering, T., Schnetz, E., Fartasch, M., Sandhoff, K., and Magin, A. M. (1999) Normal ultrastructure, but altered stratum corneum lipid and protein composition in a mouse model for epidermolytic hyperkeratosis. J. Investig. Dermatol. 113, 329–334.
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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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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 303 Fig.
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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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