PCR Detection of Microbial Pathogens PCR Detection of Microbial ...

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Pre-PCR Processing 49 56. Laigret, F., Deaville, J., Bove, J. M., and Bradbury, J. M. (1996) Specific detection of Mycoplasma iowae using polymerase chain reaction. Mol. Cell. Probes 10, 23–29. 57. Pomp, D., and Medrano, J. F. (1991) Organic solvents as facilitators of polymerase chain reaction. Biotechniques 10, 58–59. 58. Abu Al-Soud, W. (2000) Optimisation of diagnostic PCR: A study of PCR inhibitors in blood and sample pretreatment. Doctoral thesis. Department of Applied Microbiology, Lund University, Lund, Sweden. 59. Kreader, C. A. (1996) Relief of amplification inhibition in PCR with bovine serum albumin or T4 gene 32 protein. Appl. Environ. Microbiol. 62, 1102–1106. 60. Tsutsui, K., and Mueller, G.C. (1987) Hemin inhibits virion-associated reverse transcriptase of murine leukemia virus. Biochem. Biophys. Res. Commun. 149, 628–634. 61. Abu Al-Soud, W., and Rådström, P. (2000) Effects of amplification facilitators on diagnostic PCR in the presence of blood, feces, and meat. J. Clin. Microbiol. 38, 4463–4470. 62. Topal, M. D., and Sinha, N. K. (1983) Products of bacteriophage T4 genes 32 and 45 improve the accuracy of DNA replication in vitro. J. Biol. Chem. 258, 12,274–12,279. 63. Chandler, D. P., Wagnon, C. A., and Bolton, H., Jr. (1998) Reverse transcriptase (RT) inhibition of PCR at low concentrations of template and its implications for quantitative RT-PCR. Appl. Environ. Microbiol. 64, 669–677. 64. Jordan, S. P., Zugay, J., Darke, P. L. and Kuo, L. C. (1992) Activity and dimerization of human immunodeficiency virus protease as a function of solvent composition and enzyme concentration. J. Biol. Chem. 267, 20,028–20,032. 65. Wu, J. R., and Yeh, Y. C. (1973) Requirement of a functional gene 32 product of bacteriophage T4 in UV.J. Virol. 12, 758–765. 66. Varadaraj, K., and Skinner, D .M. (1994) Denaturants or cosolvents improve the specificity of PCR amplification of a G + C-rich DNA using genetically engineered DNA polymerases. Gene 140, 1–5. 67. Lee, C. H., Mizusawa, H., and Kakefuda, T. (1981) Unwinding of double-stranded DNA helix by dehydration. Proc. Natl. Acad. Sci. USA 78, 2838–2842. 68. Dutton, C. M., Paynton, C., and Sommer, S. S. (1993) General method for amplifying regions of very high G+C content. Nucleic Acids Res. 21, 2953–2954. 69. Innis, M. A., Myambo, K. B., Gelfand, D. H., and Brow, M. A. D. (1988) DNA sequencing with Thermus aquaticus DNA polymerase and direct sequencing of polymerase chain reaction-amplified DNA. Proc. Nat. Acad. Sci. USA 85, 9436–9440. 70. Frackman, S., Kobs, G., Simpson, D., and Storts, D. (1998) Betaine and DMSO: Enhancing agents for PCR. Promega Notes 27. 71. Henke, W., Herdel, K., Jung, K., Schnorr, D., and Loening, S.A. (1997) Betaine improves the PCR amplification of GC-rich DNA sequences. Nucleic Acids Res. 25, 3957–3958. 72. Back, J. F., Oakenfull, D., and Smith, M. B. (1979) Increased thermal stability of proteins in the presence of sugars and polyols. Biochemistry 18, 5191–5196.
50 Rådström et al. 73. Nagai, M., Yoshida, A., and Sato, N. (1998) Additive effects of bovine serum albumin, dithiothreitol, and glycerol on PCR. Biochem. Mol. Biol. Int. 44, 157–163. 74. Demeke, T., and Adams, R.P. (1992) The effects of plant polysaccharides and buffer additives on PCR. Biotechniques 12, 332–334. 75. Kim, S., Labbe, R. G., and Ryu, S. (2000) Inhibitory effects of collagen on the PCR for detection of Clostridium perfringens. Appl. Environ. Microbiol. 66, 1213–1215. 76. Chen, S., Yee, A., Griffiths, M., et al. (1997) The evaluation of a fluorogenic polymerase chain reaction assay for the detection of Salmonella species in food commodities. Int. J. Food. Microbiol. 35, 239–250. 77. Knutsson, R., Fontanesi, F., Grage, H., and Rådström, P. (2001) Development of a PCRcompatible enrichment medium for Yersinia enterocolitica: Amplification precision and dynamic detection range during cultivation. Int. J. Food Microbiol. 72, 185–201. 78. Grant, K. A., Dickinson, J. H., Payne, M. J., Campbell, S., Collins, M. D., and Kroll, R. G. (1993) Use of the polymerase chain reaction and 16S rRNA sequences for the rapid detection of Brochothrix spp. in foods. J. Appl. Bacteriol. 74, 260–267. 79. Klein, P. G., and Juneja, V. K. (1997) Sensitive detection of viable Listeria monocytogenes by reverse transcription-PCR. Appl. Environ. Microbiol. 63, 4441–4448. 80. Nordvåg, B., Riise, H., Husby, G., Nilsen, I., and El-Gewely, M. R. (1995) Direct use of blood in PCR. Methods Neurosci. 26, 15–25. 81. Seesod, N., Lundeberg, J., Hedrum, A., et al. (1993) Immunomagnetic purification to facilitate DNA diagnosis of Plasmodium falciparum. J. Clin. Microbiol. 31, 2715–2719. 82. Lantz, P. -G., Tjerneld, F., Borch, E., Hahn-Hägerdal, B., and Rådström, P. (1994) Enhanced sensitivity in PCR detection of Listeria monocytogenes in soft cheese through use of an aqueous two-phase system as a sample preparation method. Appl. Environ. Microbiol. 60, 3416–3418. 83. Giambernardi, T. A., Rodeck, U., and Klebe, R. J. (1998) Bovine serum albumin reverses inhibition of RT-PCR by melanin. Biotechniques 25, 564–566. 84. Sidhu, M. K., Liao, M. J., and Rashidbaigi, A. (1996) Dimethyl sulfoxide improves RNA amplification. Biotechniques 21, 44–47.
Page 1 and 2: TM Methods in Molecular Biology VOL
Page 3 and 4: 4 Sachse 2. Selection of Target Seq
Page 5 and 6: Table 1 Target Sequences Used in PC
Page 7 and 8: 8 Sachse Fig. 1. Structural organiz
Page 9 and 10: 10 Sachse proteins (66-68), invasio
Page 11 and 12: 12 Sachse Since there appears to be
Page 13 and 14: 14 Sachse In the context of identif
Page 15 and 16: 16 Sachse to partially compensate t
Page 17 and 18: 18 Sachse nostic potential of PCR.
Page 19 and 20: 20 Sachse product has to be confirm
Page 21 and 22: 22 Sachse 7. van Camp, G., Fierens,
Page 23 and 24: 24 Sachse 33. Rappelli, P., Are, R.
Page 25 and 26: 26 Sachse 60. Furrer, B., Candrian,
Page 27 and 28: 28 Sachse 89. Bloch, W. (1991) A bi
Page 29 and 30: 30 Sachse
Page 31 and 32: 32 Rådström et al. Fig. 1. Illust
Page 33 and 34: 34 Rådström et al. immunoglobulin
Page 35 and 36: 36 Rådström et al. and the captur
Page 37 and 38: Table 2 Comparison of the Performan
Page 39 and 40: 40 Rådström et al. explain these
Page 41 and 42: 42 Rådström et al. 5.1. Proteins
Page 43 and 44: 44 Rådström et al. neous. Consequ
Page 45 and 46: 46 Rådström et al. 11. Powell, H.
Page 47: 48 Rådström et al. 39. Katcher, H
Page 51 and 52: 52 Hoorfar and Cook 2. FOOD-PCR: A
Page 53 and 54: 54 Hoorfar and Cook Fig. 2. Practic
Page 55 and 56: 56 Hoorfar and Cook Fig. 4. The str
Page 57 and 58: Table 58 3 Hoorfar and Cook Test Co
Page 59 and 60: 60 Hoorfar and Cook The choosing an
Page 61 and 62: 62 Hoorfar and Cook 10. Demanding L
Page 63 and 64: 64 Hoorfar and Cook 15. Anon. (1995
Page 65 and 66: 66 Lübeck and Hoorfar ods for the
Page 67 and 68: 68 Lübeck and Hoorfar amplificatio
Page 69 and 70: 70 Lübeck and Hoorfar It may be ne
Page 71 and 72: 72 Lübeck and Hoorfar specificity
Page 73 and 74: 74 Lübeck and Hoorfar The latter i
Page 75 and 76: 76 Lübeck and Hoorfar A simple che
Page 77 and 78: 78 Lübeck and Hoorfar 13. Hanai, K
Page 79 and 80: 80 Lübeck and Hoorfar 43. Mitchell
Page 81 and 82: 82 Lübeck and Hoorfar 70. Lawrence
Page 83 and 84: 84 Lübeck and Hoorfar 98. Lantz, P
Page 85 and 86: 88 Frey Table 1 Presence of the Var
Page 87 and 88: 90 Frey 13. Lysis buffer: 100 mM Tr
Page 89 and 90: 92 Frey as template for PCR. In add
Page 91 and 92: 94 Frey strains, including all sero
Page 93 and 94: 96 Frey
Page 95 and 96: 98 Ewalt and Bricker (named for the
Page 97 and 98: 100 Ewalt and Bricker 4. Ethidium b
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102 Ewalt and Bricker Primer Cockta
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104 Ewalt and Bricker Fig. 2. Typic
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106 Ewalt and Bricker with betaine
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108 Ewalt and Bricker unused ethidi
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110 Englen et al. which campylobact
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112 Englen et al. 18. Dehydrated cu
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114 Englen et al. 3.1.3. Fecal Samp
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116 Englen et al. respectively), an
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118 Englen et al. Fig. 1. Identific
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120 Englen et al. 3. Goossens, H.,
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122 Englen et al.
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124 Sachse and Hotzel Table 1 Compa
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126 Sachse and Hotzel Table 2 Prime
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128 Sachse and Hotzel 7. Phenol: sa
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130 Sachse and Hotzel 4. Vortex mix
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132 Sachse and Hotzel Fig. 2. Speci
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134 Sachse and Hotzel In the latter
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136 Sachse and Hotzel 17. Longbotto
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138 Popoff spastic paralysis. The g
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Table 3 Primers for Toxin Gene Dete
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142 Popoff 18. Agarose gel loading
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144 Popoff Taq reaction buffer 1X,
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146 Popoff almost all C. perfringen
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148 Popoff 2. Add to each PCR tube
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150 Popoff 7. Hielm, S., Hyyttia, E
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152 Popoff 35. Wieckowski, E., Bill
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154 Berri et al. 2. Materials 1. C.
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156 Berri et al. 3.3.2. Vaginal Swa
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158 Berri et al. Fig. 1. Trans-PCR.
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160 Berri et al. Fig. 3. Sensitivit
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162 Berri et al.
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164 Gallien The first description o
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166 Gallien
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168 Gallien 2. Materials 2.1. Bacte
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170 Gallien 10. Ethidium bromide: 1
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Table 2 Components (in µL) of 25-
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Table 4 Components (in µL) of 25-
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176 Gallien 3.3. Specific Isolation
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Table 6 PCR Conditions for Subtypin
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180 Gallien Fig. 3. Photographic im
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182 Gallien 3. Boyce, T. G., Swerdl
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184 Gallien enteropathogenic E. col
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186 O'Connor This chapter will desc
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188 O'Connor 2.2. PCR of Enriched F
Page 187 and 188:
190 O'Connor 4. Notes 1. In enrichi
Page 189 and 190:
192 O'Connor 4. O’Sullivan, N., F
Page 191 and 192:
194 Lester and LeFebvre titers (4).
Page 193 and 194:
196 Lester and LeFebvre 3.1.2. Samp
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Fig. 1. Sensitivity of the PCR assa
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200 Lester and LeFebvre 5. Swart, K
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202 Skuce et al. Table 1 Significan
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204 Skuce et al. commercial kits. E
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206 Skuce et al. Fig. 1. Schematic
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208 Skuce et al. 5. Disposable ster
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210 Skuce et al. 2.5.2. Sequence An
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212 Skuce et al. 2. Carefully trans
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Table 4 Recommended PCR Amplificati
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216 Skuce et al. Fig. 3. PCR produc
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218 Skuce et al. Fig. 5. Spoligotyp
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220 Skuce et al. 14. Aranaz, A., Li
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222 Skuce et al.
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224 Khan Simultaneous detection of
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226 Khan 10. Incubate for 20 min at
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228 Khan 5. Periodically, multiplex
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230 Khan
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232 Hotzel et al. tis (2). Particul
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234 Hotzel et al. 8. Sodium dodecyl
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236 Hotzel et al. 3. Methods 3.1. D
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238 Hotzel et al. 3.1.5. Semen (see
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240 Hotzel et al. Fig. 1 Detection
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242 Hotzel et al. 4. Notes 1. The u
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244 Hotzel et al. in Mycoplasma Pro
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246 Hotzel et al.
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248 Kobisch and Frey PCR assay to d
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250 Kobisch and Frey Table 1 Oligon
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252 Kobisch and Frey 3.2.1. Prepara
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254 Kobisch and Frey First round of
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256 Kobisch and Frey References 1.
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258 Christensen et al. thrombotic m
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260 Christensen et al. Table 1 Spec
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Table 2 Oligonucleotide Primers for
Page 261 and 262:
264 Christensen et al. 3.2. Extract
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Table 3 PCR Protocols for the Patho
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268 Christensen et al. 2. Apply fra
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270 Christensen et al. 7. To reduce
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272 Christensen et al. 24. Fisher,
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274 Christensen et al. 54. Hunt, M.
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276 Malorny and Helmuth valent meta
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278 Malorny and Helmuth 12. Apparat
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280 Malorny and Helmuth 3.3. Amplif
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282 Malorny and Helmuth Table 2 Vol
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284 Malorny and Helmuth Table 4 PCR
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286 Malorny and Helmuth 3. Wallace,
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288 Malorny and Helmuth
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290 Wastling and Mattsson is an imp
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292 Wastling and Mattsson 2. Remove
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294 Wastling and Mattsson Fig. 1. B
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296 Wastling and Mattsson time PCR
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298 Wastling and Mattsson
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300 Pozio and La Rosa Table 1 Princ
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302 Pozio and La Rosa regions; spot
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304 Pozio and La Rosa 3. Proteinase
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306 Pozio and La Rosa Table 3 PCR-R
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308 Pozio and La Rosa 2. Pepsin sho
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310 Pozio and La Rosa
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312 Knutsson and Rådström The ref
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314 Knutsson and Rådström Fig. 1.
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316 Knutsson and Rådström 2.4. El
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318 Knutsson and Rådström the swa
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320 Knutsson and Rådström Fig. 3.
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322 Knutsson and Rådström 4. Alek
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324 Knutsson and Rådström 34. Hee
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