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Cloning Gene Family Members 497 3. Preston, G. M. (1993) Use of degenerate oligonucleotide primers and the polymerase chain reaction to clone gene family members, in Methods in Molecular Biology, vol. 15: PCR Protocols: Current Methods and Applications. (White, B. A., ed.) Humana, Totowa, NJ, pp. 317–337. 4. Preston, G. M. and Agre, P. (1991) Isolation of the cDNA for erythrocyte integral membrane protein of 28 kilodaltons: Member of an ancient channel family. Proc. Natl. Acad. Sci. USA 88, 11,110–11,114. 5. Wada, K.-N., Aota, S.-I., Tsuchiya, R., Ishibashi, F., Gojobori, T., and Ikemura, T. (1990) Codon usage tabulated from the GenBank genetic sequence data. Nucleic Acids Res. 18, 2367–2411. 6. Preston, G. M., Carroll, T. P., Guggino, W. B., and Agre, P. (1992) Appearance of water channels in Xenopus oocytes expressing red cell CHIP28 protein. Science 256, 385–387. 7. Chrispeels, M. J. and Agre, P. (1994) Aquaporins: Water channel proteins of plant and animal cells. TIBS 19, 421– 425. 8. Jung, J. S., Bhat, B. V., Preston, G. M., Guggino, W. B., Baraban, J. M., and Agre P. (1994) Molecular characterization of an aquaporin cDNA from brain: candidate osmoreceptor and regulator of water balance. Proc. Natl. Acad. Sci. USA 91, 13,052–13,056. 9. Raina, S., Preston, G. M., Guggino, W. B., and Agre, P. (1995) Molecular cloning and characterization of an aquaporin cDNA from salivary, lacrimal and respiratory tissues. J. Biol. Chem. 270, 1908–1912. 10. Knoth, K., Roberds, S., Poteet, C., and Tamkun, M. (1988) Highly degenerate, inosinecontaining primers specifically amplify rare cDNA using the polymerase chain reaction. Nucleic Acids Res. 16, 10,932. 11. Chérif-Zahar, B., Bloy, C., Kim, C. L. V., Blanchard, D., Bailly, P., Hermand, P., et al. (1990) Molecular cloning and protein structure of a human blood group Rh polypeptide. Proc. Natl. Acad. Sci. USA 87, 6243–6247. 12. Sambrook, J., Fritsch, E. F., and Maniatis, T., eds. (1989) Molecular Cloning: A Laboratory Manual. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY. 13. Ausubel, F. M., Brent, R., Kingston, R. E., Moore, D. D., Seidman, J. G., Smith, J. A., et al., eds. (1994) Current Protocols in Molecular Biology. Greene Publishing/Wiley-Interscience, New York. 14. Wistow, G. J., Pisano, M. M., and Chepelinsky, A. B. (1991) Tandem sequence repeats in transmembrane channel proteins. TIBS 16, 170–171. 15. Jung, J. S., Preston, G. M., Smith, B. L., Guggino, W. B., and Agre, P. (1994) Molecular structure of the water channel through aquaporin CHIP: The hourglass model. J. Biol. Chem. 269, 14,648–14,654. 16. Nielsen, S., Smith, B. L., Christensen, E. I., and Agre, P. (1993) Distribution of the aquaporin CHIP in secretory and resorptive epithelia and capillary endothelia. Proc. Natl. Acad. Sci. USA 90, 7275–7279. 17. Smith, B. L., Preston, G. M., Spring, F. A., Anstee, D. J., and Agre, P. (1994) Human red cell Aquaporin CHIP, I. molecular characterization of ABH and Colton blood group antigens. J. Clin. Invest. 94, 1043–1049. 18. Preston, G. M., Smith, B. L., Zeidel, M. L., Moulds, J. J., and Agre, P. (1994) Mutations in aquaporin-1 in phenotypically normal humans without functional CHIP water channels. Science 265, 1585–1587. 19. Weyant, R. S., Edmonds, P., and Swaminathan, B. (1990) Effects of ionic and nonionic detergents on the Taq polymerase. Biotechnology 9, 308–309. 20. Bookstein, R., Lai, C.-C., To, H., and Lee, W.-H. (1990) PCR-based detection of a polymorphic BamHI site in intron 1 of the human retinoblastoma (RB) gene. Nucleic Acids Res. 18, 1666.
498 Preston 21. Hung, T., Mak, K., and Fong, K. (1990) A specificity enhancer for polymerase chain reaction. Nucleic Acids Res. 18, 4953. 22. Zhao, Z.-Y. and Joho, R. H. (1990) Isolation of distantly related members in a multigene family using the polymerase chain reaction technique. Biochem. Biophys. Res. Commun. 167, 174–182. 23. Aelst, L. V., Hohmann, S., Zimmermann, F. K., Jans, A. W. H., and Thevelein, J. M. (1991) A yeast homologue of the bovine lens fiber MIP gene family complements the growth defect of a Saccharomyces cerevisiae mutant on fermentable sugars but not its defect in glucose-induced RAS-mediated cAMP signalling. EMBO J. 10, 2095–2104. 25. Muramatsu, S. and Mizuno, T. (1989) Nucleotide sequence of the region encompassing the glpKF operon and its upstream region containing a bent DNA sequence of Escherichia coli. Nucleic Acids Res. 17, 4378. 25. Höfte, H., Hubbard, L., Reizer, J., Ludevid, D., Herman, E. M., and Chrispeels, M. J. (1992) Vegetative and seed-specific forms of Tonoplast Intrinsic Protein in the vacuolar membrane of Arabidopsis thaliana. Plant Physiol. 99, 561–570. 26. Fushimi, K., Uchida, S., Hara, Y., Hirata, Y., Marumo, F., and Sasaki, S. (1993) Cloning and expression of apical membrane water channel of rat kidney collecting tubule. Nature 361, 549–552. 27. Gorin, M. B., Yancey, S. B., Cline, J., Revel, J.-R., and Horwitz, J. (1984) The major intrinsic protein (MIP) of the bovine lens fiber membrane: characterization and structure based on cDNA cloning. Cell 39, 49–59. 28. Guerrero, F. D., Jones, J. T., and Mullet, J. E. (1990) Turgor-responsive gene transcription and RNA levels increase rapidly when pea shoots are wilted: sequence and expression of three induced genes. Plant Mol. Biol. 15, 11–26. 29. Rao, Y., Jan, L. Y., and Jan, Y. N. (1990) Similarity of the product of the Drosophila neurogenic gene big brain to transmembrane channel proteins. Nature 345, 163–167. 30. Fortin, M. G., Morrison, N. A., and Verma, D. P. S. (1987) Nodulin-26, a peribacteroid membrane nodulin is expressed independently of the development of the peribacteroid compartment. Nucleic Acids Res. 15, 813–824. 31. Feng, D.-F. and Doolittle, R. F. (1990) Progressive alignment and phylogenetic tree construction of protein sequences, in Methods in Enzymology, vol. 183: Molecular Evolution: Computer Analysis of Protein and Nucleic Acid Sequences (Doolittle, R. F., ed.), Academic, New York, pp. 375–387.
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63. Primed In Situ Nucleic Acid Lab
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4 Bartlett and Stirling The thing t
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6 Bartlett and Stirling Fig. 2. Res
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8 Carroll and Casimir of PCR. Such
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10 Carroll and Casimir cost more th
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12 Carroll and Casimir are no longe
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14 Carroll and Casimir Should these
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16 McDonagh Fig. 1. Unidirectional
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18 McDonagh stored. This means that
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20 McDonagh
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22 Stirling which will either not a
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24 Stirling
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28 Bartlett References 1. US Depart
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30 Bartlett and White 11. 5 M sodiu
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32 Bartlett and White
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34 Pearson and Stirling 11. Microfu
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36 Going 3. Methods 3.1. Section Cu
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38 Going pipet filler. Spread the p
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40 Going digitally to record the di
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42 Going
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44 Pearson 7. Add 60 µL of chlorof
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46 Bartlett 3. Methods 3.1. RNA Ext
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48 Pearson 3. Method The method of
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50 Stirling and Bartlett 4. Protein
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52 Stirling and Bartlett
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54 Stirling 3. Methods 3.1. Fungal
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56 McDonagh 2. Add 0.4 mL of TNE bu
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58 Schmerer 2. Materials To apply t
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60 Schmerer 3. The additional purif
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62 Schmerer
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64 Stirling
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66 Bartlett Table 1 Recommended Aga
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68 Bartlett Table 2 Separation of D
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70 Bartlett 2. 5× TBE: 54 g of Tri
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72 Bartlett 7. Remove upper aqueous
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74 Bartlett 4. Many modern electrop
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76 Bartlett
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78 Stirling 11. Store at -20°C for
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82 Hyndman and Mitsuhashi 3.1. Effi
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84 Hyndman and Mitsuhashi Fig. 1. H
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86 Hyndman and Mitsuhashi Fig. 3. H
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88 Hyndman and Mitsuhashi can be ge
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90 Grunenwald may be affected by ea
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92 Grunenwald 50°C will generally
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94 Grunenwald of template DNA, a su
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96 Grunenwald than absolutely neces
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98 Grunenwald 2. Foord, O. S. and R
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100 Grunenwald
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102 Stirling Table 1 Thermal Cycler
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104 Stirling
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106 Wang and Young full-length cDNA
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108 Wang and Young Fig. 1. (A) Nort
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110 Wang and Young Fig. 3. Expresse
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112 Wang and Young 2. First-strand
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114 Wang and Young 3′-RACE outlin
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116 Wang and Young
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118 Dassanayake and Samaranayake co
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120 Dassanayake and Samaranayake 5.
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122 Dassanayake and Samaranayake Re
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124 Iannone et al. Fig. 1. Diagram
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Table 1 Oligonucleotides Descriptio
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128 Iannone et al. 5. For microsphe
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130 Iannone et al. 4. To adjust for
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132 Iannone et al. 6. Target concen
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134 Iannone et al.
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136 Benjamin, Smith, and Waites amp
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138 Benjamin, Smith, and Waites the
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140 Benjamin, Smith, and Waites 2.2
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142 Benjamin, Smith, and Waites 2.
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148 Benjamin, Smith, and Waites 8.
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150 Benjamin, Smith, and Waites
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152 Olmos et al. Fig. 1. RT-hemines
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154 Olmos et al. This nested RT-PCR
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156 Olmos et al. Table 2 Volume and
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158 Olmos et al. 8. The sensitivity
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160 Olmos et al.
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162 Abe 5. Moloney murine leukemia
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164 Abe Table 2 Detection Rate of H
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166 Abe 4. For HBV, nested PCR usin
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168 Tellier et al. of Pfu (and ther
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170 Tellier et al. 2. Cline, J., Br
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172 Tellier et al. 38. Tamiya, S.,
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174 Tellier et al. 13. Thin-wall PC
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176 Tellier et al. 13 min for the l
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178 Tellier et al.
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182 Stirling efficiency of the reac
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184 Stirling
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186 Cremer and Moos Fig. 1. Rearran
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188 Cremer and Moos 4. Count cells
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190 Cremer and Moos Fig. 3. Alignme
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192 Cremer and Moos Fig. 4. Testing
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194 Cremer and Moos 5. Compare the
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196 Cremer and Moos 11. Klein, E.,
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198 McDonagh the dilution method is
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200 McDonagh 2.2. Basic PCR 1. dNTP
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202 McDonagh Fig. 2. Quantitative P
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204 McDonagh
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206 Bartlett Table 1 Example Assay
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208 Bartlett 3.4. Calculation of Re
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210 Bartlett 11. Cerenkov counting
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212 Kerr Fig. 1. Fluorescent probes
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214 Kerr after the PCR. This reduce
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218 Bartlett As with any experiment
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220 Bartlett Even once novel regula
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222 Bartlett Notwithstanding these
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224 Bartlett
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226 Dominguez et al. Table 1 Primer
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228 Dominguez et al. 4. Oligonucleo
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230 Dominguez et al. Fig. 2. cDNA n
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232 Dominguez et al. 3.4. Gel Elect
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234 Dominguez et al. 3. If the cont
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236 Dominguez et al. 11. Joshi, C.
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238 Khalturin, Kuznetsov, and Bosch
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246 Ringquist et al. In this chapte
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248 Ringquist et al. 5. Total RNA s
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250 Ringquist et al. 3. Purificatio
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252 Ringquist et al. 2. The present
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254 Ringquist et al.
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256 Case-Green, Pritchard, and Sout
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272 Oien Fig. 1. A schematic diagra
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274 Oien 4. 100% and 70% ethanol. 5
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276 Oien 2. Purify polyA + mRNA fro
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278 Oien 50-mL conical tubes. Resus
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280 Oien Forward Primer, and then r
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282 Oien 8. PCR. With SAGE, achievi
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284 Oien
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288 Edwards and Bartlett technology
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290 Edwards and Bartlett ing less p
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292 Edwards and Bartlett Stepwise m
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294 Edwards and Bartlett
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296 Rithidech and Dunn 11. Ethidium
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298 Rithidech and Dunn Fig. 1. PCR
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300 Rithidech and Dunn
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302 Edwards and Bartlett Studies th
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304 Edwards and Bartlett 11. Hot st
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306 Edwards and Bartlett Fig. 1. Ex
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308 Edwards and Bartlett 3. Sartor,
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310 Schmerer the investigation conc
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312 Schmerer References 1. Kunkel,
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314 Schmerer
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316 Aubele and Smida 2.2. Chemicals
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318 Aubele and Smida References 1.
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320 Nakashima, Akahoshi, and Tanaka
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322 Nakashima, Akahoshi, and Tanaka
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324 Stirling 9. TAE (20×): 484 g o
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326 Stirling
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328 Han and Robinson Fig. 1. Basic
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330 Han and Robinson sequence diffe
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332 Han and Robinson 4. Notes 1. PC
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334 Han and Robinson
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338 Stirling of simple and improved
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340 Stirling concentrations interfe
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342 Daniels to sequence a 500-bp PC
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344 Daniels 4. Load all of the samp
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346 Daniels References 1. Orita, M.
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348 Kösel et al. Fig. 1. Schematic
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350 Kösel et al. 3. Methods 3.1. P
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352 Kösel et al. Fig. 2. Sequencin
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354 Kösel et al. 5. Kwok, S. and H
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356 Mazars and Theillet Fig. 1. Sch
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358 Mazars and Theillet of genomic
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360 Mazars and Theillet
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362 Suomalainen and Syvänen Fig. 1
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364 Suomalainen and Syvänen detect
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366 Suomalainen and Syvänen temper
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368 Shen et al. ladder. Also, direc
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370 Shen et al. 3. Mineral oil. 4.
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372 Shen et al. extended primers, w
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374 Quivy and Becker Fig. 1. The us
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376 Quivy and Becker that decreases
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378 Quivy and Becker 2. Solution of
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380 Quivy and Becker 7. Precipitate
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382 Quivy and Becker 7. Prepare a p
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384 Quivy and Becker
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386 Walsh by most, but not all M13
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388 Walsh PCR products are now flus
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390 Walsh 5. For palindromic restri
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392 Walsh
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394 McAleer, Coffey, and Dunham Fig
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396 McAleer, Coffey, and Dunham Tab
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398 McAleer, Coffey, and Dunham Tab
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400 McAleer, Coffey, and Dunham
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402 Stirling 5. Homopolymer Regions
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406 Speel, Ramaekers, and Hopman Ta
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408 Speel, Ramaekers, and Hopman Fi
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410 Speel, Ramaekers, and Hopman po
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Table 2 Comparison of PRINS, in Sit
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414 Speel, Ramaekers, and Hopman te
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Table 3 Summary of Control Experime
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418 Speel, Ramaekers, and Hopman 3.
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420 Speel, Ramaekers, and Hopman ad
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422 Speel, Ramaekers, and Hopman 25
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424 Speel, Ramaekers, and Hopman 63
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426 Bull and Paskins Fig. 1. Result
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428 Bull and Paskins 2.3. Detection
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430 Bull and Paskins 6. Shake the s
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432 Bull and Paskins
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434 Wiedorn and Goldmann Fig. 1. IS
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436 Wiedorn and Goldmann 41. Protei
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438 Wiedorn and Goldmann 2. Incubat
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440 Wiedorn and Goldmann 3.15. Prim
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442 Wiedorn and Goldmann ficient se
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Page 457 and 458: 470 Wang 2. Materials 2.1. PCR 1. D
Page 459 and 460: 472 Wang Fig. 1. A brief outline of
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Page 473 and 474: 486 Preston amplification approach
Page 475 and 476: 488 Preston 1. 10× PCR buffer: 100
Page 477 and 478: 490 Preston Fig. 1. Design of degen
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Page 481 and 482: 494 Preston 3.3. Cloning and DNA Se
Page 483: 496 Preston MgCl 2 concentrations b
Page 487 and 488: 500 Ravassard et al. Fig. 1. Constr
Page 489 and 490: 502 Ravassard et al. size dispersio
Page 491 and 492: 504 Ravassard et al. 9. ddH 2 O. 10
Page 493 and 494: 506 Ravassard et al. 3.2.2. RNA Mix
Page 495 and 496: 508 Ravassard et al. 4. Wash twice
Page 497 and 498: 510 Ravassard et al.
Page 499 and 500: 512 Pont-Kingdon Fig. 1. Constructi
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Page 503 and 504: 516 Pont-Kingdon
Page 505 and 506: 518 Jones and Winistorfer Fig. 1. D
Page 507 and 508: 520 Jones and Winistorfer Fig. 2. D
Page 509 and 510: 522 Jones and Winistorfer The yield
Page 511 and 512: 524 Jones and Winistorfer 7. Goulde
Page 513 and 514: 526 Burke and Barik Fig. 1. The bas
Page 515 and 516: 528 Burke and Barik concentration o
Page 517 and 518: 530 Burke and Barik purified mutant
Page 519: 532 Burke and Barik
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